CUBIST PHARMACEUTICALS INC
10-K, 1998-03-20
PHARMACEUTICAL PREPARATIONS
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                UNITED STATES SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549

                                    FORM 10-K

                  FOR ANNUAL AND TRANSITION REPORTS PURSUANT TO
           SECTION 13 OR 15(D) OF THE SECURITIES EXCHANGE ACT OF 1934

 /X/ ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE 
     ACT OF 1934
                  For the fiscal year ended: December 31, 1997

 / / TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES 
     EXCHANGE ACT OF 1934
     For the transition period from: _________________ to _________________

                         Commission file number: 0-21379

                          Cubist Pharmaceuticals, Inc.
             (Exact name of registrant as specified in its charter)

                 Delaware                         22-3192085
      (State or other jurisdiction of          (I.R.S. Employer
       incorporation or organization)         Identification No.)

                      24 Emily Street, Cambridge, MA 02139
              (Address of principal executive offices and Zip Code)

                                 (617) 576-1999
              (Registrant's telephone number, including area code)

          Securities registered pursuant to Section 12(b) of the Act:
                                      None

           Securities registered pursuant to Section 12(g) of the Act:
                          Common Stock, $.001 par value
                                (Title of Class)

         Indicate by check mark whether the registrant (1) has filed all reports
required to be filed by Section 13 or 15(d) of the Securities Exchange Act of
1934 during the preceding 12 months (or for such shorter period that the
registrant was required to file such reports), and (2) has been subject to such
filing requirements for the past 90 days. Yes /X/ No / /

         Indicate by check mark if disclosure of delinquent filers pursuant to
Item 405 of Regulation S-X is not contained herein, and will not be contained,
to the best of registrant's knowledge, in definitive proxy or information
statements incorporated by reference in Part III of this Form 10-K or any
amendment to this Form 10-K. / /

         The aggregate market value of the registrant's common stock, $.001 par
value per share ("Common Stock"), held by non-affiliates of the registrant as of
March 3, 1998 was approximately $30,956,565 based on 5,759,361 shares held by
such non-affiliates at the closing price of a share of Common Stock of $5.375 as
reported on the Nasdaq National Market on such date. Affiliates of the Company
(defined as officers, directors and owners of 10 percent or more of the
outstanding share of Common Stock) owned 4,821,541 shares of Common Stock
outstanding on such date. The number of outstanding shares of Common Stock of
the Company on March 3, 1998 was 10,580,902.

                       DOCUMENTS INCORPORATED BY REFERENCE

         Portions of the registrant's definitive Proxy Statement to be delivered
to stockholders in connection with the Annual Meeting of Stockholders to be held
on May 21, 1998 are incorporated by reference into Part III hereof. With the
exception of the portions of such Proxy Statement expressly incorporated into
this Annual Report on Form 10-K by reference, such Proxy Statement shall not be
deemed filed as part of this Annual Report on Form 10-K.


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                          CUBIST PHARMACEUTICALS, INC.
                           ANNUAL REPORT ON FORM 10-K

                               Table of Contents

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<CAPTION>
Item                                                                                                        Page
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<S>          <C>                                                                                            <C>
Part I

  1          Business......................................................................................... 3
  2          Description of Property .........................................................................24
  3          Legal Proceedings................................................................................24
  4          Submission of Matters to a Vote of Security Holders..............................................24

Part II

  5          Market For Registrant's Common Stock and Related Stockholder Matters.............................24
  6          Selected Financial Data..........................................................................25
  7          Management's Discussion and Analysis of Financial Condition and Results
              of Operations...................................................................................26
  7A         Quantitative and Qualitative Disclosures About Market Risk.......................................32

  8         Financial Statements and Supplementary Data.......................................................32
  9         Changes in and Disagreements With Accountants on Accounting and Financial
            Disclosure........................................................................................47

Part III

 10          Directors and Executive Officers of the Registrant...............................................48
 11          Executive Compensation...........................................................................48
 12          Security Ownership of Certain Beneficial Owners and Management...................................48
 13          Certain Relationships and Related Transactions...................................................48

Part IV

 14          Exhibits, Financial Statement Schedules, and Reports on Form 8-K.................................48

             Signatures.......................................................................................51

</TABLE>

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         Except for the historical information contained herein, this Annual
Report on Form 10-K may contain "forward-looking statements" within the meaning
of Section 27A of the Securities Act of 1933 and Section 21E of the Securities
Exchange Act of 1934, including, but not limited to, (i) statements about the
adequacy of the Company's cash, cash equivalents, other capital resources,
interest income, other income and future revenues due under the Company's
collaborative agreements to fund its operating expenses and capital requirements
as currently planned through mid-1999, (ii) statements about the amount of
capital expenditures that the Company expects to incur in 1998, (iii) statements
about the Company's plans to begin clinical trials of daptomycin in the fourth
quarter of 1998 or the first quarter of 1999, and (iv) certain statements
identified or qualified by words such as "likely", "will", "suggests", "may",
"would", "could", "should", "expects", "anticipates", "estimates", "plans",
"projects", "believes", or similar expressions (and variants of such words or
expressions). Investors are cautioned that forward-looking statements are
inherently uncertain. Actual performance and results of operations may differ
materially from those projected or suggested in the forward-looking statements
due to certain risks and uncertainties, including, but not limited to, the risks
and uncertainties described or discussed in the section "Risk Factors" in this
Annual Report on Form 10-K. The forward-looking statements contained herein
represent the Company's judgment as of the date of this Annual Report on Form
10K, and the Company cautions readers not to place undue reliance on such
statements.

PART I

ITEM 1.           BUSINESS

The Company

         Cubist Pharmaceuticals, Inc. ("Cubist" or the "Company") is a
biopharmaceutical company focused on the discovery, development and
commercialization of novel small molecule antiinfectives to treat drug resistant
pathogens. The acceleration of the Company's process to discover and develop
novel compounds is executed by screening novel genomic target assays to identify
new lead compounds and optimizing these compounds into development candidates,
developing in-licensed drug candidates and balancing risk with pharmaceutical
and technology collaborations.

Overview of Infectious Disease and Drug Resistance

         Infectious diseases are caused by bacteria and fungi present in the
environment that enter the body through the skin or mucous membranes of the
lungs, nasal passages or gastrointestinal tract, and overwhelm the body's immune
system. These pathogens then establish themselves in various tissues and organs
throughout the body and cause a number of serious and, in some cases, lethal
infections, including those of the bloodstream, heart, lung, liver and urinary
tract.

         Antiinfective drugs have, in many cases, proven highly successful in
controlling the serious morbidity and mortality that accompany these infections.
These drugs work by chemically binding to specific targets in a bacterial or
fungal pathogen, thereby inhibiting a 



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cell function essential to its survival. Currently available antiinfective drugs
can be divided into the following four broad categories, according to the type
of essential cell function they inhibit: (i) protein synthesis (e.g.,
tetracyclines, macrolides and aminoglycosides), (ii) cell wall and membrane
synthesis (e.g., penicillins, cephalosporins, carbapenems, glycopeptides and
polyenes), (iii) nucleic acid synthesis (e.g., fluoroquinolones) and (iv) cell
metabolism (e.g., trimethoprim, sulfonamides, azoles and allylamines).

         Recently, there has been a rise in the incidence of infectious diseases
caused by bacteria and fungi that have developed resistance to existing
antiinfective drugs. This phenomenon has been well documented in the medical
literature. A number of serious pathogens such as Staphylococcus aureus,
Streptococcus pneumoniae, Enterococcus faecalis, Enterococcus faecium,
Escherichia coli, Haemophilus influenzae, Pseudomonas aeruginosa, Mycobacterium
tuberculosis, Candida albicans, Aspergillus fumigatus and Aspergillus flavus
have shown significant evidence of drug resistance.

         The increasing prevalence of antiinfective drug resistance is a natural
outcome of the use and overuse of antiinfective drugs. When bacteria or fungi
are exposed to an antiinfective drug, the drug kills or attenuates the growth of
the susceptible pathogen. However, any variant in the bacterial population that
has spontaneously undergone a genetic change that confers drug resistance will
have a selective growth advantage, which is known in evolutionary terms as
natural selection. Thus, the antiinfective drug does not technically cause the
resistance but creates a situation in which the resistant pathogen can multiply
in the presence of the drug, increasing the population approximately a
millionfold in a day and quickly becoming the predominant microorganism. These
resistant bacteria can then spread rapidly from the infected patient to healthy
individuals.

         Bacteria and fungi have evolved multiple resistance mechanisms against
currently available categories of antiinfective drugs. These mechanisms include:
(i) utilization of an enzyme to alter the drug's structure by creating or
destroying chemical bonds, (ii) modification of the cell membrane to block entry
of the drug, (iii) utilization of a protein to pump the drug out of their cells
before the drug binds to the target and (iv) alteration of the target to
significantly limit the ability of the antiinfective drug to bind to the target.
Bacteria and fungi change the target by mutation of the target's protein
sequence, by chemical modification of the target structure or by the acquisition
of a new gene from another pathogen that substitutes for the target function.

         Traditional drug discovery approaches have not met the challenge posed
by drug-resistant pathogens. To date, biology-based approaches have attempted to
identify compounds that kill or attenuate the growth of the pathogen using
whole-cell screening assays. This approach is limited because compounds that
could effectively inhibit a target function inside the cell, but are unable to
penetrate cell membranes, are not identified by whole-cell screening assays.
Thus, entire classes of effective inhibitors of intracellular targets, which
could be modified by medicinal chemistry to penetrate cell membranes, have
potentially been overlooked. Chemistry-based approaches have focused on
chemically modifying the molecular structure of existing antiinfective drugs or
combining existing antiinfective drugs with another agent (an antibiotic
potentiator) to circumvent established drug resistance mechanisms. Despite the
introduction of second and third generation 



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antiinfective drugs, certain pathogens have developed resistance to all
currently available drugs. Examples include:

         Methicillin resistant Staphylococcus aureus ("MRSA"): S. aureus is a
common bacterial pathogen causing skin infections and colonization of the nares
(entrance to the nose). It is also a frequent hospital-borne pathogen, and
routinely acquires characteristics of drug resistance, virulence and toxicity
through bacterial genetic transfer. MRSA strains can cause severe tissue damage
to existing wounds and bacteremia (blood-borne infections), which has a 42%
mortality rate.

         Vancomycin resistant enterococci ("VRE"): Vancomycin is regarded by
many medical practitioners as the "last line of defense" against virulent
Gram-positive bacteria species. The emergence of VRE strains in the 1990's has
led to infections for which no approved therapy exists. Vancomycin resistance is
found in both Enterococcus faecium and Enterococcus faecalis. Resulting VRE
bacteremia has a 55% mortality rate.

         Vancomycin intermediate susceptible Staphyloccus aureus ("VISA"): The
first reports of S. aureus infections with decreased susceptibility to
vancomycin therapy occurred in 1997. Such bacterial strains have been found in a
wide geographical area throughout Japan and North America. Resistance
progression from VISA is expected to be the emergence of fully drug resistant S.
aureus strains that the medical community has long feared.

Cubist Development Program
Daptomycin

         Daptomycin, the Company's lead product, is a novel antiinfective agent
with bactericidal activity against all major Gram-positive bacteria. The
compound has already demonstrated safety and efficacy in Phase II clinical
trials, and is currently being developed in both intravenous ("IV") and oral
formulations to treat infections and colonizations, respectively, in
hospitalized patients. Cubist plans to initiate Phase III clinical trials of IV
daptomycin for the treatment of skin and skin structure and urinary tract
infections in late 1998 or early 1999, subject to Food and Drug Administration
("FDA") approval. Early clinical trials with the oral formulation of daptomycin
for the eradication of VRE from the gastrointestinal tract are planned for 1999.
Daptomycin is an antiinfective agent believed to bind to lipoteichoic acid and
disrupt the cell membrane. Because daptomycin utilizes a novel target for its
antimicrobial activity, there is no "built-in" resistance mechanism in existing
bacterial populations. Daptomycin has already been shown to be effective against
pathogens that have developed resistance to conventional antibiotics.

         In February of 1998, the Company contracted with ACS Dobfar of Milan,
Italy to manufacture daptomycin. The Company estimates initial delivery of GMP
daptomycin for clinical trial use in the fourth quarter and plans to begin
clinical trials soon thereafter.

Intravenous Product:

         In Phase II clinical studies conducted to date, IV daptomycin has
demonstrated safety and efficacy for the treatment of skin and skin structure
infections caused by Gram-positive 



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bacteria such as S. aureus and Streptococcus pyogenes. Approximately 300
subjects have received various doses of IV daptomycin in Phase I and II trials.
Approximately 70% of the multiple dose regimens administered were at a dose of 2
mg/kg per day or higher. No toxicity was experienced at doses between 2 mg/kg
per day and 6 mg/kg per day. Daptomycin was associated with minimal, reversible
muscle toxicity at dose levels of 8 mg/kg per day in 2 of 5 volunteers. All
signs of muscle toxicity subsided within several days of discontinuation of
treatment. Daptomycin has shown promising in vitro activity against
life-threatening drug resistant pathogens, including MRSA, VRE and VISA.

         At a dose of 2 mg/kg per day, daptomycin was comparable to conventional
therapy in the treatment of Gram positive infections, particularly skin and skin
structure infections with a 96.8% favorable response and may exhibit greater
efficacy than conventional therapy against resistant bacterial infections. The
Company plans to commence Phase III clinical trials in late 1998 or early 1999
to treat skin and skin structure infections and urinary tract infections,
subject to FDA approval.

 Oral Product:

         A growing problem in healthcare is the spread of drug resistant
infections from patient to patient within the hospital environment. Transmission
of VRE often leads to bacterial colonization of the gastrointestinal tract in
medical and surgical patients, and can lead to subsequent systemic infections
with high mortality rates.

         The Company is developing oral daptomycin to eradicate VRE from the
gastrointestinal tract prior to the occurrence of a potential systemic
infection. The gastrointestinal tract is one of the sources of VRE that can
cause skin, soft tissue and urinary tract infections which can lead to
bacteremia. Cubist plans to enter early clinical trials in 1999, subject to FDA
approval.

         The Company estimates between 40,000 and 200,000 hospitalized patients
in the United States require isolation due to VRE colonization each year.

The Cubist Discovery Program

         Cubist is identifying novel chemical classes of compounds that inhibit
new targets in bacteria or fungi resulting in impaired cell growth or pathogen
killing. The Company expects that drugs inhibiting these new targets would be
immediately effective against currently drug-resistant bacteria and fungi since
these pathogens have not had an opportunity to evolve resistance specific to
these new drugs. In addition, the Company is developing and implementing novel
technologies to accelerate this process of drug discovery.

         To discover novel antiinfectives for clinical development, the Cubist
discovery platform integrates the scientific disciplines and technologies
required for target validation and assay development, high-throughput screening
and medicinal chemistry.



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Target Validation and Assay Development

         The genomics explosion has resulted in the identification of a wealth
of novel targets for drug discovery. There is a great need, at the earliest
point in the discovery process to select the best targets from among the many
available. The Company utilizes its proprietary CubeBiotools(TM) bioinformatics
software to process and analyze microbial genomics information for target
identification. Targets are chosen for further development based upon an
evaluation of genetic, biochemical and microbial physiology data. The Company
has developed VITATm, a technology to expeditiously validate targets for
antiinfective drug therapy by analyzing the inhibition of a target during an
established infection in a mouse model system using a method that has analogies
to how an antibiotic inhibits it's target during an infection. The Company is
currently focusing on implementing the technology to validate targets from
clinically relevant pathogens such as Staphylococcus aureus.

         To date, the Company has developed over 100 proprietary antiinfective
target assays that are currently being utilized in the discovery and
characterization of lead compounds. The Company has broadened its target
pipeline beyond its initial program based upon the aminoacyl-tRNA synthetase
enzymes to include targets from a variety of functional areas. Some of the
essential functions these targets play a role in include tRNA processing,
protein synthesis, protein secretion, DNA replication, protein targeting and
protein translocation. These assays were developed from organisms including
Staphylococcus aureus, Enterococcus faecalis, Escherichia coli, Streptococcus
pneumoniae, Haemophilus influenzae, Mycobacterium tuberculosis and Helicobacter
pylori bacteria, Candida albicans and Pneumocystis carinii fungi and cultured
human cells. A series of secondary and tertiary screens have also been developed
to analyze compounds for whole cell activity and intracellular mechanism of
action.

High Throughput Screening

Cubist utilizes state of the art technologies in automation, robotics and assay
technologies to perform high-throughput screening of compound libraries to
identify novel inhibitors. Thousands of compounds a day are screened in these
assays. Inhibitors are further characterized using Cubist's secondary screening
assays where increasingly stringent selection criteria are applied to identify
drug candidates with the greatest potential for successful development.

         Molecules used in the Cubist screening program currently originate from
four sources: (i) Cubist's proprietary rational design chemistry programs, (ii)
Cubist's proprietary combinatorial chemistry programs, (iii) academic and
industrial collaborations and (iv) commercial sources. Selection of these
compounds was intended to provide broad chemical diversity and include compound
classes which have traditionally yielded antibacterial and antifungal compounds.
The Cubist combinatorial chemistry program generates two types of libraries,
general and lead-specific. The general libraries are designed to provide Cubist
with a diversity of molecular structures which can be used in conjunction with
high-throughput screening to identify novel lead compounds which inhibit
selected targets. Cubist constructs lead-specific libraries based on principles
of rational drug design using structural templates demonstrated to interact with
the target enzymes. A relational database is utilized to manage and analyze the
high-throughput screening data and chemical compound structure information.



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Medicinal Chemistry

Cubist optimizes the pharmaceutical properties of lead compounds, which have
been identified by its high-throughput screening through the iterative use of
medicinal chemistry and in vitro biological assays. The Company's medicinal
chemistry efforts are directed towards increasing the throughput of synthesis of
optimized analogues of specific lead compounds utilizing chemical technologies
including focused arrays, combinatorial libraries and computational chemistry.
Lead compounds enter a high-speed chemical analoging program which generates
large numbers of structurally-related compounds. Analogs are evaluated for
numerous biological properties including (i) spectrum of inhibitory potency
against a given enzyme from a variety of pathogens, (ii) selectivity for the
pathogen target versus the human homolog, (iii) inhibitory potency against
multiple targets from a single pathogen and (iv) spectrum of activity against
whole cells, including drug-resistant strains, to determine potential clinical
indication. Cubist subsequently evaluates, in animal models, drug candidates
exhibiting suitable potency, spectrum and selectivity to determine their
pharmacological and toxicological properties. Novel chemical classes of leads
with potent and selective enzyme activity and whole cell activity have been
selected for focused optimization utilizing these technologies and are the basis
of current medicinal chemistry programs.

The breadth and depth of the target validation and assay development program in
combination with the high throughput screening capacity and medicinal chemistry
optimization technologies provide multiple opportunities to discover novel
chemical classes of antiinfectives.

Collaborative Agreements

                  The Company has entered into drug discovery and development
collaboration agreements with Bristol-Myers Squibb Company ("Bristol-Myers
Squibb") and Merck & Co., Inc. ("Merck") to discover and develop novel
antiinfectives. In these collaborations, the collaborators' respective compound
libraries are screened against certain Cubist aminoacyl-tRNA synthetase targets.
Chemical compound structures are optimized into pre-clinical and clinical
development candidates. These collaborations have provided the Company with
funding, research and development resources, and access to libraries of diverse
compounds and clinical development, manufacturing and commercialization
capabilities. Through December 31, 1997, these collaborative partners and others
have provided the Company with $8.1 million of funding in the form of research
support payments, technology licensing fees and milestone payments and with a
$4.0 million equity investment.

         Bristol-Myers Squibb

         In June 1996, Cubist and Bristol-Myers Squibb entered into a
Collaborative Research and License Agreement (the "Bristol-Myers Squibb
Agreement") pursuant to which they agreed to collaborate to discover and develop
novel antiinfective drugs from leads obtained 



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by screening six of Cubist's aminoacyl-tRNA synthetase targets against
Bristol-Myers Squibb's compound library. In connection with the collaboration,
Bristol-Myers Squibb has made a $4.0 million equity investment in Cubist, has
made $1.5 million in milestone payments and has made research support payments
to Cubist. See "Management's Discussion and Analysis of Financial Condition and
Results of Operations - Results of Operations." Under the terms of the
Bristol-Myers Squibb Agreement, Cubist is entitled to receive additional
research support payments and, if certain milestones are achieved, additional
milestone payments from Bristol-Myers Squibb. Cubist has granted to
Bristol-Myers Squibb an exclusive worldwide license to commercialize drugs
resulting from this collaboration. The development, manufacture and worldwide
sale of drugs resulting from the collaboration will be conducted by
Bristol-Myers Squibb, and Cubist will be entitled to receive royalties on the
worldwide sales of any drug developed and commercialized from this
collaboration.

         Merck

         In June 1996, the Company and Merck entered into a Collaborative
Research and License Agreement (the "Merck Agreement") pursuant to which they
agreed to collaborate to discover and develop novel antiinfective drugs from
leads obtained by screening three of Cubist's aminoacyl-tRNA synthetase targets
against Merck's compound library. In connection with the collaboration, Merck
has made research support payments and has paid technology licensing fees to
Cubist. See "Management's Discussion and Analysis of Financial Condition and
Results of Operations - Results of Operations." Under the terms of the Merck
Agreement, Cubist is entitled to receive additional research support payments
and, if certain milestones are achieved, milestone payments from Merck. Cubist
has granted Merck an exclusive worldwide license to commercialize drugs
resulting from this collaboration. The development, manufacture and worldwide
sale of drugs resulting from the collaboration will be conducted by Merck, and
the Company will be entitled to receive royalties on the worldwide sales of any
drug developed and commercialized from this collaboration.

Other Collaborations

         To obtain access to a diversity of chemical compounds for the Company's
internal drug discovery programs, Cubist has entered into screening agreements
with ArQule, Inc., Genzyme Corporation and Pharmacopeia, Inc. pursuant to which
Cubist screens such party's compound libraries against Cubist's proprietary
targets. Cubist has also entered into a Collaborative Research Agreement with
Novalon Pharmaceutical Corporation, a drug discovery company focused on the
development and application of novel technologies to screen genomics targets and
accelerate lead discovery. The agreement focuses on collaborative research by
Cubist and Novalon to develop and execute specific screens for antiinfective
drug discovery. Cubist will pay Novalon a percent of revenue received by Cubist
that relates to the use of the technology and currently pays a monthly payment
for research funding, salaries and supplies.



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Patents and Proprietary Technology

         The Company seeks to protect its cloned targets, assays, organic
synthetic processes, lead compounds, screening technology and certain other
technology by, among other things, filing, or causing to be filed on its behalf,
patent applications. Cubist has three issued U.S. patents, 18 pending U.S.
patent applications and one pending international patent application. To date,
the Company has received a notice of allowance for nine of these U.S.
applications. Cubist has also licensed three U.S. patents. There can be no
assurance that patents will be granted with respect to any of the Company's
pending patent applications or with respect to any patent applications filed by
the Company in the future.

         The commercial success of the Company will depend in part on not
infringing patents or proprietary rights of others. There can be no assurance
that the Company will be able to obtain a license to any third-party technology
it may require to conduct its business or that if obtainable, such technology
can be licensed at reasonable cost. Failure by the Company to obtain a license
to technology that it may require to utilize its technologies or commercialize
its products may have a material adverse effect on the Company's business,
operating results and financial condition. In some cases, litigation or other
proceedings may be necessary to defend against or assert claims of infringement,
to enforce patents issued to the Company, to protect trade secrets, know-how or
other intellectual property rights owned by the Company, or to determine the
scope and validity of the proprietary rights of third parties. Any potential
litigation could result in substantial costs to and diversion of resources by
the Company and could have a material adverse effect on the Company's business,
operating results and financial condition. There can be no assurance that any of
the Company's issued or licensed patents would ultimately be held valid or that
efforts to defend any of its patents, trade secrets, know-how or other
intellectual property rights would be successful. An adverse outcome in any such
litigation or proceeding could subject the Company to significant liabilities,
require the Company to cease using the subject technology or require the Company
to license the subject technology from the third party, all of which could have
a material adverse effect on the Company's business, operating results and
financial condition.

         Much of the know-how of importance to the Company's technology and many
of its processes are dependent upon the knowledge, experience and skills, which
are not patentable, of key scientific and technical personnel. To protect its
rights to and to maintain the confidentiality of trade secrets and proprietary
information, the Company requires employees, Scientific Advisory Board members,
consultants and collaborators to execute confidentiality and invention
assignment agreements upon commencement of a relationship with the Company.
These agreements prohibit the disclosure of confidential information to anyone
outside the Company and require disclosure and assignment to the Company of
ideas, developments, discoveries and inventions made by employees, advisors,
consultants and collaborators. There can be no assurance, however, that these
agreements will not be breached or that the Company's trade secrets or
proprietary information will not otherwise become known or developed
independently by others.



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Government Regulation

         Overview

         The development, manufacture and marketing of drugs (including
antibiotics) developed by the Company or its collaborative partners are subject
to regulation by numerous governmental agencies in the United States,
principally the FDA, by state and local governments, and in some instances by
foreign governments. Pursuant to the Federal Food, Drug, and Cosmetic Act and
the regulations promulgated thereunder (the "FDC Act"), the FDA regulates the
pre-clinical and clinical trials, safety, effectiveness, manufacture, labeling,
storage, distribution, and promotion of drugs. Product development and approval
within the FDA regulatory framework usually takes a significant number of years,
involves the expenditure of substantial capital resources and is uncertain.

         U.S. Regulatory Process

         Before testing in the United States of any compounds with potential
therapeutic value in human test subjects may begin, stringent government
requirements for preclinical data must be satisfied. Pre-clinical testing
includes both in vitro and in vivo laboratory evaluation and characterization of
the safety and efficacy of a drug and its formulation. Pre-clinical testing
results obtained from studies in several animal species, as well as from in
vitro studies, are submitted to the FDA as part of an investigational new drug
application ("IND") and are reviewed by the FDA prior to the commencement of
human clinical trials. These pre-clinical data must provide an adequate basis
for evaluating both the safety and the scientific rationale for the initial
(Phase I) studies in human volunteers. Unless the FDA objects to an IND, the IND
becomes effective 30 days following its receipt by the FDA. Once trials have
commenced, the FDA may stop the trials by placing them on "clinical hold"
because of concerns about, for example, the safety of the product being tested.

         Clinical trials involve the administration of the drug to healthy human
volunteers or to patients under the supervision of a qualified investigator,
usually a physician, pursuant to an FDA-reviewed protocol. Human clinical trials
are typically conducted in three sequential phases, although the phases may
overlap with one another. Clinical trials must be conducted under protocols that
detail the objectives of the study, the parameters to be used to monitor safety
and the efficacy criteria to be evaluated. Each protocol must be submitted to
the FDA as part of the IND.

         Phase I clinical trials represent the initial administration of the
investigational drug to a small group of healthy human subjects or, more rarely,
to a group of selected patients with the targeted disease or disorder. The goal
of Phase I clinical trials is typically to test for safety (adverse effects),
dose tolerance, absorption, biodistribution, metabolism, excretion and clinical
pharmacology and, if possible, to gain early evidence regarding efficacy.

         Phase II clinical trials involve a small sample of the actual intended
patient population and seek to assess the efficacy of the drug for specific
targeted indications, to 



                                       11
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determine dose tolerance and the optimal dose range and to gather additional
information relating to safety and potential adverse effects.

         Once an investigational drug is found to have some efficacy and an
acceptable safety profile in the targeted patient population, Phase III clinical
trials are initiated to establish further clinical safety and efficacy of the
investigational drug in a broader sample of the general patient population at
geographically dispersed study sites in order to determine the overall
risk-benefit ratio of the drug and to provide an adequate basis for product
labeling. The Phase III clinical development program consists of expanded,
large-scale studies of patients with the target disease or disorder, to obtain
definitive statistical evidence of the efficacy and safety of the proposed
product and dosage regimen. All of the phases of clinical studies must be
conducted in conformance with the FDA's bioresearch monitoring regulations.

         All data obtained from a comprehensive development program including
research and product development, manufacturing, pre-clinical and clinical
trials and related information are submitted in a new drug application ("NDA")
to the FDA and the corresponding agencies in other countries for review and
approval. In addition to reports of the trials conducted under the IND
application, the NDA includes information pertaining to the preparation of the
new drug or antibiotic, analytical methods, details of the manufacture of
finished products and proposed product packaging and labeling. Although the FDC
Act requires the FDA to review NDAs within 180 days of their filing, in practice
longer times may be required. The FDA also frequently requests that additional
information be submitted, requiring significant additional review time. Any
proposed product of the Company likely would be subject to demanding and
time-consuming NDA approval procedures in virtually all countries where
marketing of the products is intended. These regulations define not only the
form and content of safety and efficacy data regarding the proposed product but
also impose specific requirements regarding manufacture of the product, quality
assurance, packaging, storage, documentation and recordkeeping, labeling,
advertising and marketing procedures.

         The FDA has developed two "fast track" policies for certain new drugs,
one policy for expedited development and review, and one policy for accelerated
approval. The expedited review policy applies to new drug therapies, including
antibiotics, that are intended to treat persons with life-threatening and
severely-debilitating illnesses, especially where no satisfactory alternative
therapy exists. The FDA has defined "severely-debilitating" to mean diseases or
conditions that cause major irreversible morbidity. During the developmental
stage of drugs that qualify, the FDA expedites consultation and review of these
experimental therapies.

         The FDA's accelerated approval policy applies to certain new drug or
antibiotic products that have been studied for their safety and effectiveness in
treating serious or life-threatening illnesses and that provide "meaningful
therapeutic benefit to patients over existing treatments." This accelerated
approval, or fast track approach, is generally limited to new drugs or
antibiotics that treat patients that are unresponsive to, or intolerant of,
available therapy, or when there is improved patient response over currently
available therapy. The accelerated approval policy is further limited to drugs
for which the predictive value of the surrogate endpoint, in terms of clinical
outcome, has not been established. At 



                                       12
<PAGE>

the time of approval, the FDA may grant approval on a surrogate endpoint or an
effect on a clinical endpoint other than survival or irreversible morbidity. The
FDA may impose certain restrictions on distribution, limiting its use to certain
facilities or specialty-trained physicians or making its use contingent on the
performance of certain specified medical procedures. Postmarketing studies
(Phase IV trials) are usually required to further affirm safety and/or efficacy.
However, if an acceptable clinical endpoint has been established, the drug must
be evaluated for approval under the traditional (non-fast track) approach.

         The Company is also subject to regulation under other federal laws and
regulation under state and local laws, including laws relating to occupational
safety, laboratory practices, the use, handling and disposition of radioactive
materials, environmental protection and hazardous substance control. Although
the Company believes that its safety procedures for handling and disposing of
radioactive compounds and other hazardous materials used in its research and
development activities comply with the standards prescribed by federal, state
and local regulations, the risk of accidental contamination or injury from these
materials cannot be completely eliminated. In the event of any such accident,
the Company could be held liable for any damages that result and any such
liability could exceed the resources of the Company.

Competition

         The biotechnology and pharmaceutical industries are intensely
competitive and subject to rapid and significant technological change.
Competitors of the Company in the United States and elsewhere are numerous and
include, among others, major, multinational pharmaceutical and chemical
companies, specialized biotechnology firms and universities and other research
institutions. Many of these competitors employ greater financial and other
resources, including larger research and development staffs and more effective
marketing and manufacturing organizations, than the Company or its collaborative
partners. Acquisitions of competing companies and potential competitors by large
pharmaceutical companies or others could enhance financial, marketing and other
resources available to such competitors. As a result of academic and government
institutions becoming increasingly aware of the commercial value of their
research findings, such institutions are more likely to enter into exclusive
licensing agreements with commercial enterprises, including competitors of the
Company, to market commercial products. There can be no assurance that the
Company's competitors will not succeed in developing technologies and drugs that
are more effective or less costly than any which are being developed by the
Company or which would render the Company's technology and future drugs obsolete
and noncompetitive.

         In addition, some of the Company's competitors have greater experience
than the Company in conducting pre-clinical and clinical trials and obtaining
FDA and other regulatory approvals. Accordingly, the Company's competitors may
succeed in obtaining FDA or other regulatory approvals for drug candidates more
rapidly than the Company. Companies that complete clinical trials, obtain
required regulatory agency approvals and commence commercial sale of their drugs
before their competitors may achieve a significant competitive advantage,
including certain patent and FDA marketing exclusivity rights that would delay
the Company's ability to market certain products. There can be no assurance 



                                       13
<PAGE>

that drugs resulting from the Company's research and development efforts, or
from the joint efforts of the Company and its collaborative partners, will be
able to compete successfully with competitors' existing products or products
under development or that they will obtain regulatory approval in the United
States or elsewhere.

Employees

         As of February 20, 1998, the Company had 66 full-time employees, 50 of
whom were engaged in research and development and 16 of whom were engaged in
management, administration and finance. Doctorates are held by 26 of the
Company's employees. The Company's employees are not covered by a collective
bargaining agreement. The Company has never experienced an employment-related
work stoppage and considers its employee relations to be good.




Executive Officers of the Registrant

         The executive officers of the Company are as follows:

<TABLE>
<CAPTION>

Name                                     Age   Position
- -------------------------------        -----   ------------------------------------
<S>                                    <C>     <C>
Scott M. Rocklage, Ph.D.                 43    President, Chief Executive
                                                Officer and Director

Francis P. Tally, M.D.                   57    Executive Vice President, Scientific
                                                Affairs

Mark P. Carthy                           37    Vice President and Chief Business
                                                Officer

Dennis D. Keith, Ph.D.                   54    Vice President, Drug Discovery

</TABLE>

                                       14
<PAGE>

<TABLE>
<CAPTION>
Name                                     Age   Position
- -------------------------------        -----   ------------------------------------
<S>                                    <C>     <C>
Frederick B. Oleson, Jr., D.Sc.          49    Vice President, Drug Development

Thomas A. Shea                           38    Senior Director of Finance &
                                                Administration,
                                                Treasurer
</TABLE>

         Dr. Rocklage has served as President and Chief Executive Officer and as
a member of the Board of Directors of the Company since July 1994. From 1990 to
1994, Dr. Rocklage served as President and Chief Executive Officer of Nycomed
Salutar, Inc., a diagnostic imaging company. From 1992 to 1994, he also served
as President and Chief Executive Officer and Chairman of Nycomed Interventional,
Inc., a medical device company. From 1986 to 1990, he served in various
positions at Salutar, Inc., a diagnostic imaging company and was responsible for
designing and implementing research and development programs that resulted in
three drug products in human clinical trials, including the approved drugs
Omniscan and Teslascan. Dr. Rocklage received his B.S. in Chemistry from the
University of California, Berkeley and his Ph.D. in Chemistry from the
Massachusetts Institute of Technology.

         Mr. Carthy has served as Vice President and Chief Business Officer
since April 1997. Mr. Carthy joined Cubist from Vertex Pharmaceuticals Inc., a
biotechnology company, where he served most recently as Senior Director of
Business Development. Prior to joining Vertex, Mr. Carthy managed the chemical
filtration business for Millipore and was a member of the Mergers and
Acquisitions Department at Shearson Lehman Hutton. Mr. Carthy holds a Masters
Degree in Chemical Engineering from the University of Missouri and a Masters in
Business Administration from Harvard Business School.

         Dr. Tally has served as Executive Vice President, Scientific Affairs
since January 1997. From March 1995 to January 1997, he served the Company as
Vice President of Research and Development. From 1986 to 1995, Dr. Tally served
as Executive Director of Infectious Disease, Molecular Biology and Natural
Products Research at the Lederle Laboratories of American Cyanamid/American Home
Products, where he was responsible for worldwide clinical studies for
piperacillin/tazobactam which was registered for sales in Europe in 1992,
approved by the FDA in 1993 and marketed as Zosyn. From 1975 to 1986, he served
as Senior Physician in Infectious Disease at the New England Medical Center and
Associate Professor of Medicine at Tufts Medical Center. Dr. Tally received his
A.B. in Biology from Providence College and his M.D. from George Washington
University School of Medicine.

         Dr. Keith has served as Vice President, Drug Discovery since October
1997. Dr. Keith joined Cubist from Hoffman-La Roche Inc. where he served in
various positions from 1971-1997, the most recent of which was Director of
Antiinfective Chemistry. Dr. Keith received his B.S. in Chemistry from Bates
College and his Ph.D. in Organic Chemistry from Yale University.



                                       15
<PAGE>

         Dr. Oleson has served as Vice President, Drug Development since
November 1997. Prior to joining Cubist, Dr. Oleson served as an independent
consultant from June 1997 to November 1997; Director of Preclinical Research at
AutoImmune, Inc., a biotechnology company, from January 1997 to June 1997;
Director, Toxicology and Preclinical Pharmacology at Biogen, Inc., a
biotechnology company, from 1992 to 1997 and in various positions at
Bristol-Myers Squibb from 1983 to 1992. Dr. Oleson was a key contributor in the
development of the Biogen drug AVONEX and a key consultant in the development of
Hirulog for The Medicines Company. Dr. Oleson received his B.S. in Biochemistry
from Princeton University and a Doctor of Science in Physiology/Radiation
Biology from Harvard University School of Public Health.

         Mr. Shea has served as Treasurer and Chief Accounting Officer since
June 1996 and has served as Senior Director of Finance and Administration since
December 1997. Previous to that he was Director of Finance and Administration.
From 1987 to 1993, he served as Manager of Accounting/MIS and Budget and
Financial Analyst at ImmuLogic Pharmaceutical Corporation, a biotechnology
company. Mr. Shea received his B.S. in Accounting/Law from Babson College and
his Masters in Business Administration from Suffolk University.





Risk Factors

         Stockholders and prospective purchasers of the Company's Common Stock
should carefully consider the following risk factors, in addition to the other
information appearing in this Annual Report on Form 10-K.

         Early Stage of Product Development; No Assurance of Successful
Commercialization. Since inception, the Company has generated no revenue from
product sales. The Company's research and development programs are at an early
stage, and the Company does not expect that any drugs resulting from its
research and development efforts, or from the joint efforts of the Company and
its collaborative partners, will be commercially available for a significant
number of years, if at all. The Company has one drug candidate in preclinical
development and is currently in the process of optimizing lead candidates to
select other drug candidates for preclinical development. To date, the Company
has not, independently or with its collaborative partners, completed the
optimization of any lead candidates. Any drug candidates developed by the
Company will require significant additional research and development efforts,
including extensive preclinical (animal and in vitro data) and clinical testing
and regulatory approval, prior to commercial sale. Only one of the Company's
drug candidates has advanced to any phase of preclinical or clinical trials.
There can be no assurance that the Company's approach to drug discovery, acting
independently or with the efforts of any collaborative partner of the Company,
will be 



                                       16
<PAGE>

effective or will result in the development of any drug. The Company's drug
candidates will be subject to the risks of failure inherent in the development
of pharmaceutical products based on new technologies. These risks include the
possibilities that any or all of the Company's drug candidates will be found to
be unsafe, ineffective or toxic or otherwise fail to meet applicable regulatory
standards or receive necessary regulatory clearances; that these drug
candidates, if safe and effective, will be difficult to develop into
commercially viable drugs or to manufacture on a large scale or will be
uneconomical to market; that proprietary rights of third parties will preclude
the Company from marketing such drugs; or that third parties will market
superior or equivalent drugs. The failure to develop safe, commercially viable
drugs would have a material adverse effect on the Company's business, operating
results and financial condition.

         Uncertainty Due to Unproven Technology. The Company's drug discovery
approach faces technical issues which have not been resolved and requires the
development of multiple novel technologies to create a successful drug
candidate. While the Company has demonstrated that certain compounds have the
ability to inhibit the activity of certain molecular targets, the Company has
not proven that this activity can be utilized clinically as a therapeutic.
Furthermore, there can be no assurance that the inhibitory activity already
demonstrated in primary screening will continue to be encouraging in further
screening or drug discovery studies. The Company has not tested any drug
candidates developed from the Company's drug discovery program in humans, and
there can be no assurance that there will be clinical benefits associated with
any such drug candidates. Furthermore, there can be no assurance that the
Company will successfully address these technological challenges or others that
may arise in the course of development. Any failure of the Company to anticipate
or respond adequately to technological developments will have a material adverse
effect on the Company's business, operating results and financial condition.
There can be no assurance that the Company will be able to employ its drug
discovery approach successfully.

         Dependence on Collaborative Partners and Others. A key element of the
Company's strategy is to enhance certain of its drug discovery and development
programs and to fund its capital requirements, in part, by entering into
collaborative agreements with major pharmaceutical companies. The Company is a
party to collaborative agreements with Bristol-Myers Squibb and Merck
(collectively, the "Collaborative Agreements"). Under the Collaborative
Agreements, each of Bristol-Myers Squibb and Merck is responsible for (i)
providing libraries of compounds for screening against certain of the Company's
aminoacyl-tRNA synthetase targets, (ii) selecting, in collaboration with Cubist,
compounds determined to be leads in the screening for subsequent development,
(iii) conducting preclinical and clinical trials and obtaining required
regulatory approvals of drug candidates, and (iv) manufacturing and
commercializing resulting drugs. As a result, the Company's receipt of revenues
(whether in the form of continued research funding, drug development milestones
or royalties on sales) under the Collaborative Agreements is dependent upon the
decisions made by the manufacturing and marketing resources of its collaborative
partners. The Company's collaborative partners are not obligated to develop or
commercialize any drug candidates resulting from the Collaborative Agreements.
The amount and timing of resources dedicated by the Company's collaborative
partners to their respective collaborations with the Company is not within the
Company's control. Moreover, certain drug candidates discovered by the Company
may be viewed by the Company's collaborative partners as competitive with such
partners' drugs or drug candidates. Accordingly, there can 



                                       17
<PAGE>

be no assurance that the Company's collaborative partners will elect to proceed
with the development of drug candidates which the Company believes to be
promising or that they will not pursue their existing or alternative
technologies in preference to such drug candidates. There can be no assurance
that the interests of the Company will continue to coincide with those of its
collaborative partners, that some of the Company's collaborative partners will
not develop independently, or with third parties, drugs that could compete with
drugs of the types contemplated by the Collaborative Agreements, or that
disagreements over rights or technology or other proprietary interests will not
occur.

         If any of the Company's collaborative partners breaches or terminates
its agreement with the Company, or otherwise fails to conduct its collaborative
activities in a timely manner, the development or commercialization of any drug
candidate or research program under these Collaborative Agreements may be
delayed, the Company may be required to undertake unforeseen additional
responsibilities or to devote unforeseen additional resources to such
development or commercialization, or such development or commercialization could
be terminated. Any such event could materially adversely affect the Company's
financial condition, intellectual property position and operations. In addition,
there have been a significant number of recent consolidations among
pharmaceutical companies. Such consolidations among the companies with which the
Company is collaborating could result in the diminution or termination of, or
delays in, the development or commercialization of drug candidates or research
programs under one or more of the Collaborative Agreements.

         Additional Financing Requirements; Uncertainty of Available Funding.
The Company will require substantial additional funds for its drug discovery and
development programs, for operating expenses, for pursuing regulatory
clearances, for the development of manufacturing, marketing and sales
capabilities and for prosecuting and defending its intellectual property rights
before it can expect to realize significant revenues from commercial sales. The
Company intends to seek such additional funding through public or private
financing or collaborative or other arrangements with corporate partners. If
additional funds are raised by issuing equity securities, further dilution to
existing stockholders may result and future investors may be granted rights
superior to those of existing stockholders. There can be no assurance, however,
that additional financing will be available from any of these sources or, if
available, will be available on acceptable or affordable terms. If adequate
funds are not available, the Company may be required to delay, reduce the scope
of or eliminate one or more of its research and development programs or to
obtain funds by entering into arrangements with collaborative partners or others
that require the Company to issue additional equity securities or to relinquish
rights to certain technologies or drug candidates that the Company would not
otherwise issue or relinquish in order to continue independent operations. See
"Management's Discussion and Analysis of Financial Condition and Results of
Operations."

         History of Losses and Expectation of Future Losses; Uncertainty of
Future Profitability. The Company has incurred a cumulative operating loss of
approximately $23.0 million through December 31, 1997. Losses have resulted
principally from costs incurred in research and development activities related
to the Company's efforts to develop target assays, acquisition and chemical
optimization of compounds, automated high throughput screening and from the
associated administrative costs. The Company expects to incur significant
additional operating losses over the next several years and expects 



                                       18
<PAGE>

cumulative losses to increase substantially due to expanded research and
development efforts, preclinical and clinical trials and development of
manufacturing, marketing and sales capabilities. In the next few years, the
Company's revenues may be limited to research support payments under the
Collaborative Agreements and any amounts received under other research or drug
development collaborations that the Company has established or will establish.
There can be no assurance, however, that the Company will be able to establish
any additional collaborative relationships on terms acceptable to the Company or
maintain in effect the current Collaborative Agreements. The Company's ability
to achieve significant revenue or profitability is dependent on its or its
collaborative partners' ability to successfully complete the development of drug
candidates, to develop and obtain patent protection and regulatory approvals for
the drug candidates and to manufacture and commercialize the resulting drugs.
The Company will not receive revenues or royalties from commercial sales for a
significant number of years, if at all. Failure to receive significant revenues
or achieve profitable operations would impair the Company's ability to sustain
operations. There can be no assurance that the Company will ever successfully
develop, commercialize, patent, manufacture and market any products, obtain
required regulatory approvals or achieve profitability. See "Management's
Discussion and Analysis of Financial Condition and Results of Operations."

         Uncertainty of Patents and Proprietary Rights. The Company's success
will depend in part on its ability to obtain U.S. and foreign patent protection
for its drug candidates and processes, preserve its trade secrets and operate
without infringing the proprietary rights of third parties. Because of the
length of time and expense associated with bringing new drug candidates through
the development and regulatory approval process to the marketplace, the
pharmaceutical industry has traditionally placed considerable importance on
obtaining patent and trade secret protection for significant new technologies,
products and processes. There can be no assurance that any additional patents
will issue from any of the patent applications owned by, or licensed to, the
Company. Further, there can be no assurance that any rights the Company may have
under issued patents will provide the Company with significant protection
against competitive products or otherwise be commercially viable. Legal
standards relating to the validity of patents covering pharmaceutical and
biotechnological inventions and the scope of claims made under such patents are
still developing. There is no consistent policy regarding the breadth of claims
allowed in biotechnology patents. The patent position of a biotechnology firm is
highly uncertain and involves complex legal and factual questions. There can be
no assurance that any existing or future patents issued to, or licensed by, the
Company will not subsequently be challenged, infringed upon, invalidated or
circumvented by others. In addition, patents may have been granted, or may be
granted, covering products or processes that are necessary or useful to the
development of the Company's drug candidates. If the Company's drug candidates
or processes are found to infringe upon the patents, or otherwise impermissibly
utilize the intellectual property of others, the Company's development,
manufacture and sale of such drug candidates could be severely restricted or
prohibited. In such event, the Company may be required to obtain licenses from
third parties to utilize the patents or proprietary rights of others. There can
be no assurance that the Company will be able to obtain such licenses on
acceptable terms, or at all. There has been significant litigation in the
industry regarding patents and other proprietary rights. If the Company becomes
involved in litigation regarding its intellectual property rights or the
intellectual property rights of others, the 



                                       19
<PAGE>

potential cost of such litigation and the potential damages that the Company
could be required to pay could be substantial.

         In addition to patent protection, the Company relies on trade secrets,
proprietary know-how and technological advances which it seeks to protect, in
part, by confidentiality agreements with its collaborative partners, employees
and consultants. There can be no assurance that these confidentiality agreements
will not be breached, that the Company would have adequate remedies for any such
breach, or that the Company's trade secrets, proprietary know-how and
technological advances will not otherwise become known or be independently
discovered by others.

         Uncertainty Associated with Preclinical and Clinical Testing. Before
obtaining regulatory approvals for the commercial sale of any of the Company's
potential drugs, the drug candidates will be subject to extensive preclinical
and clinical trials to demonstrate their safety and efficacy in humans. The
Company is dependent on its collaborative partners to conduct clinical trials
for the drug candidates resulting from the Collaborative Agreements and may
become dependent on other third parties to conduct future clinical trials of its
internally developed drug candidates. The Company has no experience in
conducting preclinical or clinical trials, and preclinical or clinical trials
have been commenced with respect to only one of the Company's drug candidates
and none of the drug candidates being developed jointly by the Company and its
collaborative partners. Furthermore, there can be no assurance that preclinical
or clinical trials of any drug candidates will demonstrate the safety and
efficacy of such drug candidates at all or to the extent necessary to obtain
regulatory approvals. Companies in the biotechnology industry have suffered
significant setbacks in advanced clinical trials, even after demonstrating
promising results in earlier trials. The failure to adequately demonstrate the
safety and efficacy of a drug candidate under development could delay or prevent
regulatory approval of the drug candidate and would have a material adverse
effect on the Company's business, operating results and financial condition.

         No Assurance of Market Acceptance. There can be no assurance that any
drugs successfully developed by the Company, independently or with its
collaborative partners, if approved for marketing, will achieve market
acceptance. The antiinfective drugs which the Company is attempting to develop
will compete with a number of well-established antiinfective drugs manufactured
and marketed by major pharmaceutical companies. The degree of market acceptance
of any drugs developed by the Company will depend on a number of factors,
including the establishment and demonstration of the clinical efficacy and
safety of the Company's drug candidates, their potential advantage over existing
therapies and reimbursement policies of government and third-party payors. There
is no assurance that physicians, patients or the medical community in general
will accept and utilize any drugs that may be developed by the Company
independently or with its collaborative partners.

         Intense Competition. The biotechnology and pharmaceutical industries
are intensely competitive and subject to rapid and significant technological
change. Competitors of the Company in the United States and elsewhere are
numerous and include, among others, major multinational pharmaceutical and
chemical companies, specialized biotechnology firms and universities and other
research institutions. Many of these competitors employ greater financial and
other resources, including larger research and development staffs and more



                                       20
<PAGE>

effective marketing and manufacturing organizations, than the Company or its
collaborative partners. Acquisitions of competing companies and potential
competitors by large pharmaceutical companies or others could enhance financial,
marketing and other resources available to such competitors. As a result of
academic and government institutions becoming increasingly aware of the
commercial value of their research findings, such institutions are more likely
to enter into exclusive licensing agreements with commercial enterprises,
including competitors of the Company, to market commercial products. There can
be no assurance that the Company's competitors will not succeed in developing
technologies and drugs that are more effective or less costly than any which are
being developed by the Company or which would render the Company's technology
and future drugs obsolete and noncompetitive.

         In addition, some of the Company's competitors have greater experience
than the Company in conducting preclinical trials and obtaining U.S. FDA and
other regulatory approvals. Accordingly, the Company's competitors may succeed
in obtaining FDA or other regulatory approvals for drug candidates more rapidly
than the Company. Companies that complete clinical trails, obtain required
regulatory agency approvals and commence commercial sale of their drugs before
their competitors may achieve a significant competitive advantage, including
certain patent and FDA marketing exclusivity rights that would delay the
Company's ability to market certain products. There can be no assurance that
drugs resulting from the Company's research and development efforts, or from the
joint efforts of the Company and its collaborative partners, will be able to
compete successfully with competitors' existing products or products under
development or that they will obtain regulatory approval in the United States or
elsewhere.

         Impact of Extensive Government Regulation. The FDA and comparable
agencies in foreign countries impose substantial requirements upon the
introduction of pharmaceutical products through lengthy and detailed
preclinical, laboratory and clinical testing procedures, sampling activities and
other costly and time-consuming procedures to establish their safety and
efficacy. All of the Company's drug candidates will require governmental
approvals for commercialization, none of which have been obtained. Preclinical
and clinical trials and manufacturing of the Company's drug candidates will be
subject to the rigorous testing and approval processes of the FDA and
corresponding foreign regulatory authorities. Satisfaction of these requirements
typically take a significant number of years and can vary substantially based
upon the type, complexity and novelty of the product. There can be no assurance
as to when Cubist, independently or with its collaborative partners, might first
submit an IND for FDA or other regulatory review. Government regulation also
affects the manufacturing and marketing of pharmaceutical products.

         The effect of government regulation may be to delay marketing of the
Company's potential drugs for a considerable or indefinite period of time,
impose costly procedural requirements upon the Company's activities and furnish
a competitive advantage to larger companies or companies more experienced in
regulatory affairs. Delays in obtaining governmental regulatory approval could
adversely affect the Company's marketing as well as the Company's ability to
generate significant revenues from commercial sales. There can be no assurance
that FDA or other regulatory approvals for any drug candidates developed by the
Company will be granted on a timely basis or at all. Moreover, if regulatory
approval of a drug candidate is granted, such approval may impose limitations on
the indicated use 



                                       21
<PAGE>

for which such drug may be marketed. Even if initial regulatory approvals for
the Company's drug candidates are obtained, the Company, its drugs and its
manufacturing facilities would be subject to continual review and periodic
inspection, and later discovery of previously unknown problems with a drug,
manufacturer or facility may result in restrictions on such drug or
manufacturer, including withdrawal of the drug from the market. The regulatory
standards are applied stringently by the FDA and other regulatory authorities
and failure to comply can, among other things, result in fines, denial or
withdrawal of regulatory approvals, product recalls or seizures, operating
restrictions and criminal prosecution.

         The FDA has developed two "fast track" policies for certain new drugs
(including antibiotics), one policy for expedited development and review and one
policy for accelerated approval. The expedited development and review policy
applies to new drug therapies that are intended to treat persons with
life-threatening and severely debilitating illnesses, especially where no
satisfactory alternative therapy exists. The accelerated approval policy applies
to certain new drugs that are intended to treat persons with serious or
life-threatening illnesses that provide a meaningful therapeutic benefit to
patients over existing treatments. There can be no assurance that any drug
candidate contemplated by the Company will qualify for the FDA's various fast
track or priority approval policies. Nor can there be any assurance that such
policies will remain as currently implemented by the FDA. As with many
biotechnology and pharmaceutical companies, the Company is subject to numerous
environmental and safety laws and regulations. Any violation of, and the cost of
compliance with, these regulations could materially adversely affect the
Company's business, operating results and financial condition. The Company is
subject to periodic inspections and has not received notice of any material
violations of any environmental or safety law or regulation.

         Dependence on Key Personnel. The Company is highly dependent upon the
efforts of its senior management and scientific team, including its President
and Chief Executive Officer. Although Dr. Rocklage has entered into an
employment agreement with the Company, the terms of the employment agreement
provide that Dr. Rocklage may terminate his employment with the Company at any
time upon thirty days' written notice. None of the Company's other executive
officers or key employees has entered into an employment agreement with the
Company. The loss of the services of one or more of these individuals might
impede the achievement of the Company's development objectives. Because of the
specialized scientific nature of the Company's business, the Company is highly
dependent upon its ability to attract and retain qualified scientific and
technical personnel. There is intense competition among major pharmaceutical and
chemical companies, specialized biotechnology firms and universities and other
research institutions for qualified personnel in the areas of the Company's
activities. There can be no assurance that the Company will be able to continue
to attract and retain the qualified personnel necessary for the development of
its business. Loss of the services of, or failure to recruit, key scientific and
technical personnel could adversely affect the Company's business, operating
results and financial condition.

         Lack of Manufacturing, Marketing and Sales Capability and Experience.
Cubist has not yet made any significant investment in the development of
manufacturing, marketing or sales capabilities. The Company has no experience in
manufacturing of products in accordance with Good Manufacturing Practices
("GMP") as prescribed by the FDA or to 



                                       22
<PAGE>

produce an adequate supply of compounds to meet future requirements for clinical
trials. If the Company is unable to develop or contract for manufacturing
capabilities on acceptable terms, the Company's ability to conduct preclinical
and clinical trials with the Company's drug candidates will be adversely
affected, resulting in delays in the submission of drug candidates for
regulatory approvals and in the initiation of new development programs, which in
turn could materially impair Cubist's competitive position and the possibility
of achieving profitability.

         The Company has no experience in marketing drugs. The Company has
granted marketing rights to its collaborative partners with respect to drugs
developed through the Collaborative Agreements. The Company may seek to
collaborate with a third party to market those drugs for which it has retained
or licensed marketing rights or may seek to market and sell such drugs directly.
If the Company seeks to collaborate with a third party, there can be no
assurance that a collaborative agreement can be reached on acceptable terms. If
the Company seeks to market and sell such drugs directly, the Company will need
to hire additional personnel skilled in marketing and sales as it develops drugs
with commercial potential. There can be no assurance that the Company will be
able to acquire, or establish third-party relationships to provide, any or all
of these capabilities.

         Reimbursement and Drug Pricing Uncertainty. The successful
commercialization of, and the interest of potential collaborative partners to
invest in, the development of the Company's drug candidates will depend
substantially on reimbursement of the costs of the resulting drugs and related
treatments at acceptable levels from government authorities, private health
insurers and other organizations, such as health maintenance organizations
("HMOs"). There can be no assurance that reimbursement in the United States or
elsewhere will be available for any drugs the Company may develop or, if
available, will not be decreased in the future, or that reimbursement amounts
will not reduce the demand for, or the price of, the Company's drugs, thereby
adversely affecting the Company's business. If reimbursement is not available or
is available only to limited levels, there can be no assurance that the Company
will be able to obtain collaborative partners to manufacture and commercialize
drugs, or would be able to obtain a sufficient financial return on its own
manufacture and commercialization of any future drugs.

         Third-party payors are increasingly challenging the prices charged for
medical products and services. Also, the trend toward managed health care in the
United States and the concurrent growth of organizations such as HMOs, which can
control or significantly influence the purchase of health care services and
products, as well as legislative proposals to reform health care or reduce
government insurance programs, may result in lower prices for pharmaceutical
products. The cost containment measures that health care providers are
instituting, including practice protocols and guidelines and clinical pathways,
and the effect of any health care reform, could materially adversely affect the
Company's ability to sell any of its drugs if successfully developed and
approved. Moreover, the Company is unable to predict what additional legislation
or regulation, if any, relating to the health care industry or third-party
coverage and reimbursement may be enacted in the future or what effect such
legislation or regulation would have on the Company's business.

         Potential Product Liability and Availability of Insurance. The
Company's business exposes it to potential liability risks that are inherent in
the testing, manufacturing and 



                                       23
<PAGE>

marketing of pharmaceutical products. The use of the Company's drug candidates
in clinical trials may expose the Company to product liability claims and
possible adverse publicity. These risks will expand with respect to the
Company's drug candidates, if any, that receive regulatory approval for
commercial sale. Product liability insurance for the biotechnology industry is
generally expensive, if available at all. The Company does not have product
liability insurance but intends to obtain such coverage if and when its drug
candidates are tested in clinical trials. However, such coverage is becoming
increasingly expensive and there can be no assurance that the Company will be
able to obtain insurance coverage at acceptable costs or in a sufficient amount,
at all, or that a product liability claim would not adversely affect the
Company's business, operating results or financial condition.

ITEM 2.           DESCRIPTION OF PROPERTY

         The Company's headquarters and research and development facilities are
located in a 24,000 square foot facility leased by the Company in Cambridge,
Massachusetts at 24 Emily Street. The Company believes that this space will be
adequate for its research and drug development activities for at least the next
year.





ITEM 3.           LEGAL PROCEEDINGS

         The Company is not a party to any material legal proceedings.

ITEM 4.           SUBMISSION OF MATTERS TO A VOTE OF SECURITY HOLDERS

                  No matters were submitted to a vote of security holders during
the last quarter of the fiscal year ended December 31, 1997.

PART II

ITEM 5.           MARKET FOR REGISTRANTS' COMMON EQUITY AND RELATED STOCKHOLDER 
                  MATTERS

Market Information

         Since October 25, 1996, the effective date of the Company's initial
public offering, the Company's common stock has been traded on the Nasdaq
National Market under the symbol "CBST". Prior to such date, no established
public trading market existed for the Company's common stock. The following
table sets forth, for the period indicated, the high and low sale prices per
share of the Company's common stock as reported by the Nasdaq National Market.

<TABLE>
<CAPTION>
                                                               High        Low
                                                              -------    -------
<S>                                                           <C>        <C>
                      1996
    Fourth Quarter (commencing on October 25, 1996) . . . .   $  7.00     $ 5.50
                      1997
</TABLE>

                                       24
<PAGE>

<TABLE>
<CAPTION>
                                                               High        Low
                                                              -------    -------
<S>                                                           <C>        <C>

         First Quarter                                         $13.00     $ 6.00
         Second Quarter                                        $10.25     $ 6.00
         Third Quarter                                         $ 7.50     $ 5.00
         Fourth Quarter                                        $ 8.25     $ 4.88
</TABLE>

Holders

         As of March 3, 1998, the Company had approximately 150 stockholders of
record. This does not reflect persons or entitles who hold their stock in
nominee or "street" name through various brokerage firms.



Dividends

         The Company has not paid dividends on its Common Stock. The Company
anticipates it will continue to reinvest earnings to finance future growth, and
therefore does not intend to pay dividends in the foreseeable future.



Recent Sales of Unregistered Securities

         Described below is information regarding all securities of the Company
sold by the Company during the fiscal year ended December 31, 1997, which were
not registered under the Securities Act of 1933, as amended (the "Securities
Act").

         In July 1997, the Company issued and sold an aggregate of 979,591
shares of Common Stock to International Biotechnology Trust plc ("IBT") and H&Q
Capital Management ("H&Q") at a purchase price of $6.125 per share. The issuance
and sale of such shares of Common Stock were made in reliance on Section 4(2) of
the Securities Act.

ITEM. 6.          SELECTED FINANCIAL DATA


<TABLE>
<CAPTION>
                                                                  Years ended December 31,
                                                           (in thousands, except per share data)
                                                  -------------------------------------------------------
                                                     1997        1996        1995       1994       1993
                                                  ---------    --------    --------   --------   -------- 
<S>                                               <C>          <C>         <C>        <C>        <C>      
Statement of Operations Data:
Total revenues..................................  $   2,733    $  4,985    $  1,271   $   --     $   --
Research and development
 expenses .......................................     9,341       6,871       4,965      3,309      1,169
General and administrative expenses .............     3,292       1,989       1,708      1,449        547
Other income ....................................     1,833        --          --         --         --
Net loss ........................................    (7,265)     (3,799)     (5,396)    (4,813)    (1,688)
Basic and diluted net loss 
 per share ...................................... $   (0.73)   $  (1.49)   $  (5.47)  $  (7.61)  $  (3.50)
Weighted average number of common
 shares outstanding .............................     9,995       2,554         986        633        482
</TABLE>


                                       25
<PAGE>

<TABLE>
<CAPTION>
                                                                   Years ended December 31,
                                                                        (in thousands)
                                                  -------------------------------------------------------
                                                     1997        1996        1995       1994       1993
                                                  ---------    --------    --------   --------   -------- 
<S>                                               <C>          <C>         <C>        <C>        <C>      
Balance Sheet Data:
Cash and cash equivalents and short
 and long-term investments .....................  $ 18,116    $ 19,329     $ 3,056     $ 1,221   $ 4,457
Total assets ...................................    21,673      23,452       7,048       4,250     7,241
Long-term obligations ..........................     1,105       1,053       1,257       2,032     1,164
Stockholder's equity ...........................    19,063      20,299       4,895         823     5,488
</TABLE>






ITEM. 7           MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION 
                  AND RESULTS OF OPERATIONS

Overview

         Since its incorporation on May 1, 1992 and commencement of operations
in February 1993, Cubist has been engaged in the research, development and
commercialization of novel antiinfective drugs to treat infectious diseases
caused by bacteria and fungi, primarily those resistant to existing
antiinfective drugs. The Company has a limited history of operations and has
experienced significant operating losses since inception. The Company expects to
incur significant additional operating losses over the next several years and
expects cumulative losses to increase substantially due to expanded research and
development efforts, pre-clinical and clinical trials and development of
manufacturing, marketing and sales capabilities.

         A key element of the Company's strategy is to enhance certain of its
drug discovery and development programs and to fund its capital requirements, in
part, by entering into collaborative agreements with major pharmaceutical
companies. The Company is a party to collaborative agreements based specifically
on its aminoacyl-tRNA synthetase program with Bristol-Myers Squibb Company
("Bristol-Myers Squibb") and Merck & Co., Inc. ("Merck"). Under these
collaborative agreements, the Company is entitled to receive research support
payments and, if certain drug development milestones are achieved, milestone
payments. In addition, the Company will be entitled to receive royalties on
worldwide sales of any drug developed and commercialized from these
collaborations.

         On June 20, 1997, the Company's collaborative agreement with Pfizer
expired pursuant to its own terms. Prior to such expiration, the Company had
received all of the research support payments and technology licensing fees that
the Company was entitled to receive under that collaborative agreement. In
accordance with the terms of that collaborative agreement, the Company selected
and licensed from Pfizer one of the chemical compounds that was identified and
characterized during the Company's collaboration with Pfizer. Pursuant to the
terms of that license, the Company may develop and commercialize such licensed
compound without further obligation to Pfizer.



                                       26
<PAGE>

         On November 7, 1997, the Company entered into a license agreement with
Eli Lilly and Company ("Eli Lilly") pursuant to which the Company acquired
exclusive worldwide rights to develop, manufacture and market daptomycin. In
exchange for such license, the Company has paid to Eli Lilly an upfront license
fee in cash, and if certain drug development milestones are achieved, has agreed
to pay milestone payments by issuing shares of Common Stock to Eli Lilly. In
addition, the Company will be required to pay royalties to Eli Lilly on
worldwide sales of daptomycin. Daptomycin is a novel, natural product being
developed for the treatment of Staphylococcus aureus and enterococcus infections
in humans. The Company anticipates that it will begin clinical trials of
daptomycin in the fourth quarter of 1998 or the first quarter of 1999.

         The Company and Novalon Pharmaceutical Corporation ("Novalon") entered
into a collaborative research agreement on May 5, 1997 to accelerate and broaden
the development of technologies to screen genomic targets. On September 29,
1997, the Company extended its collaboration with Novalon through February 2001.
The extended collaboration will focus on utilizing these targets to identify
lead compounds active against the Company's antibacterial and antifungal
targets. In addition, the Company agreed to terminate its option to acquire
Novalon and sold its existing equity position back to Novalon for $2.0 million
resulting in a gain of $1.8 million included in other income. In connection with
such transaction, the Company was granted an option to purchase up to twenty
percent of the outstanding shares of Novalon from existing shareholders. This
option is at a price of $6.00 per share expiring in August of 1998. The Company
will pay Novalon a percent of revenues received by the Company that relates to
the use of the technology and currently pays a monthly fee for research funding
to Novalon.

         On September 25, 1997, the Company expanded its research collaboration
with Merck, adding additional aminoacyl-tRNA synthetase targets that are
proprietary to the Company and Merck's natural products compound library to the
drug discovery program. Under the terms of this expansion, Merck will pay the
Company for additional research support beyond the original agreement.

         The Company has considered the impact of the year 2000 as it relates to
the programming within the Company's computer and operating systems and does not
believe there is a significant risk to the Company.

Results of Operations

Years Ended December 31, 1997 and 1996

         Revenues. Total revenues in the year ended December 31, 1997 were
$2,733,000 compared to $4,985,000 in the year ended December 31, 1996, a
decrease of $2,252,000 or 45.2%. The revenue earned in the year ended December
31, 1997 consisted of $2,025,000 in research support funding from the
Bristol-Myers Squibb, Merck and Pfizer collaborations; a $500,000 milestone
payment from the Bristol-Myers Squibb collaboration; and $208,000 in SBIR
funding. The revenue earned in the year ended December 31, 1996 primarily
consisted of a $1,500,000 technology licensing fee from the Merck collaboration;
$2,116,000 in research support funding from the Bristol-Myers Squibb, Merck and
Pfizer collaborations; $1,000,000 in milestone payments from the Bristol-Myers
Squibb collaboration; and $369,000 in SBIR funding. The decrease in revenues in
the year ended December 31, 1997 as compared to the year 



                                       27
<PAGE>

ended December 31, 1996 was primarily due to the one-time technology license fee
from Merck in the amount of $1,500,000 in 1996; the decrease of research support
funding primarily due to the termination of the Pfizer collaboration in 1997;
and reduced milestone payments from the Bristol-Myers Squibb collaboration
during 1997.

         Research and Development Expenses. Total research and development
expenses in the year ended December 31, 1997 were $9,341,000 compared to
$6,871,000 in the year ended December 31, 1996, an increase of $2,470,000 or
35.9%. The increase was largely due to (i) amortization of the Company's
purchase option in Novalon, (ii) purchases of laboratory research supplies
associated with additional equipment, and (iii) a license fee associated with
worldwide rights to develop, manufacture and market daptomycin and expenses
associated with the development and manufacture of daptomycin from Eli Lilly,
and (iv) increased personnel and related supplies engaged in the research and
development programs.

         General and Administrative Expenses. General and administrative
expenses in the year ended December 31, 1997 were $3,292,000 compared to
$1,989,000 in the year ended December 31, 1996, an increase of $1,303,000 or
65.5%. The increase was largely due to (i) increased costs related to additional
executive staff personnel and recruiting, (ii) increased costs of premiums for
directors' and officers' insurance, (iii) increased investor and public relation
expenses and (iv) increased legal expenses primarily associated with licensing
and patent activities.

         Interest Income and Expense. Interest income in the year ended December
31, 1997 was $1,039,000 compared to $306,000 in year ended December 31, 1996, an
increase of $733,000 or 239.5%. The increase in interest income was due
primarily to higher average cash, cash equivalent and investment balances during
the year ended December 31, 1997 as compared to the year ended December 31,
1996. Interest expense in the year ended December 31, 1997 was $237,000 as
compared to $229,000 during the year ended December 31, 1996.

         Other Income. Other income in the year ended December 31, 1997 was
$1,833,000 and consisted entirely of gain on the sale of the Company's equity
position in Novalon.

         Net Loss. The net loss for the year ended December 31, 1997 was
$7,265,000 compared to $3,799,000 during the year ended December 31, 1996, an
increase of $3,466,000 or 91.2%. The increase, which was offset in part by the
gain on the sale of the Company's equity position in Novalon, was primarily due
to (i) a decrease in revenues during the year ended December 31, 1997, as
described above, (ii) an increase in expenses incurred by the Company to support
the advancement of the Company's internal research programs, (iii) an increase
in expenses incurred associated with the licensing of daptomycin from Eli Lilly,
(iv) amortization expense incurred by the Company associated with its investment
in Novalon and (v) increased costs associated with the Company's investor and
public relations program.



                                       28
<PAGE>

Results of Operations

Years ended December 31, 1996 and 1995

         Revenues. Total revenues in the year ended December 31, 1996 were
$4,985,000 compared to $1,271,000 in the year ended December 31, 1995, an
increase of $3,714,000 or 292.2%. The revenue earned in the year ended December
31, 1996 primarily consisted of $1,500,000 in technology licensing fees from the
Merck collaboration; $2,116,000 in research support funding from the
Bristol-Myers Squibb, Merck and Pfizer collaborations; $1,000,000 in milestone
payments from the Bristol-Myers Squibb collaboration; and $369,000 in SBIR
grants. In the year ended December 31, 1995, revenues consisted of $500,000 in
technology licensing fees and $488,000 in research support funding from the
Pfizer collaboration and $283,000 from SBIR Phase I grant funding.

         Research and Development Expenses. Total research and development
expenses in the year ended December 31, 1996 were $6,871,000 compared to
$4,965,000 in the year ended December 31, 1995, an increase of $1,906,000 or
38.4%. The increase was largely due to increased costs related to additional
personnel, purchases of compounds to expand the Company's compound collection
and purchases of laboratory research supplies that are utilized by such
additional personnel.

         General and Administrative Expenses. General and administrative
expenses in the year ended December 31, 1996 were $1,989,000 compared to
$1,709,000 in the year ended December 31, 1995, an increase of $280,000 or
16.4%. The increase was primarily due to costs relating to additional personnel
and recruiting, relocation, and legal expenses.

         Interest Income and Expense. Interest income in the year ended December
31, 1996 was $306,000 compared to $239,000 in the year ended December 31, 1995,
an increase of $67,000 or 28.0%. The increase in interest income was due to an
increase in the average cash, cash equivalent and investment balance during the
year ended December 31, 1996 as compared to the year ended December 31, 1995.
Interest expense was $229,000 in the year ended December 31, 1996 as compared to
$233,000 during the year ended December 31, 1995.

         Net Loss. The net loss for the year ended December 31, 1996 was
$3,799,000 compared to $5,396,000 for the year ended December 31, 1995, a
decrease of $1,597,000 or 29.6%. The decrease was primarily due to the increased
revenues associated with the Bristol-Myers Squibb, Merck and Pfizer
collaborations, which were offset only in part by additional expenses incurred
to support the advancement of the Company's internal research programs.



Liquidity and Capital Resources

         Since inception, the Company has financed its operations through the
sale of equity securities, equipment financing, sponsored research revenues,
license revenues and interest 



                                       29
<PAGE>

earned on invested capital. The Company's total cash, cash equivalent and
investments balance at December 31, 1997 was $18,116,000 compared to $19,329,000
at December 31, 1996.

         On July 18, 1997, the Company completed a private equity financing in
which the Company raised $6.0 million before offering expenses of $96,161 by
issuing 979,591 common shares at $6.125 per share.

         On September 29, 1997, the Company received a cash payment of $2.0
million from Novalon in connection with the sale of the Company's equity
position in Novalon.

         Through December 31, 1997, the Company had invested an aggregate of
$5,893,000 (of which $995,000 was invested during the year then ended) in
property and equipment, primarily in facility renovations an laboratory
equipment under capital leases. The obligations under capital leases at December
31, 1997 were $1,553,000. Minimum annual principal payments due under capital
leases total $559,000 in 1998. Principal payments are scheduled to decline each
year thereafter until expiration in 2001. The Company made principal payments
under its capital lease obligations of $695,000 in the year ended December 31,
1997. The Company expects its capital expenditures in 1998 to be approximately
$1,000,000, consisting of laboratory and other equipment purchases.

         The Company believes that its existing capital resources, interest
income and future revenues due under the Bristol-Myers Squibb and Merck
collaborative agreements will be sufficient to fund its operating expenses and
capital requirements as currently planned through mid-1999. The Company's actual
cash requirements may vary materially from those now planned and will depend on
numerous factors. There can be no assurance that the Company's existing cash,
cash equivalents, other capital resources, interest income and future revenues
due under the Bristol-Myers Squibb and Merck collaborative agreements will be
sufficient to fund its operating expenses and capital requirements during such
period. Thereafter, the Company will need to raise substantial additional
capital to fund its operations. The Company intends to seek such additional
funding through public or private financing or collaborative or other
arrangements with corporate partners.



Earnings Per Share

         Effective December 31, 1997, the Company adopted Statement of Financial
Accounting Standards 128 (SFAS 128) "Earnings per Share", which requires the
disclosure of Basic Earnings per Common Share and Diluted Earnings per Common
Share for all periods presented. At December 31, 1997, the Company had 802,468
options and 86,619 warrants outstanding. Adoption of this statement has not
affected the amounts presented in any period because the effect of including
these equity instruments would be anti-dilutive.

         Prior to the adoption of this statement, all common and common
equivalent shares issued during the twelve month period prior to the filing of
the initial public offering ("cheap stock") were included in the calculation of
basic and diluted earnings per share as if they were outstanding for all periods
presented. Adoption of this statement, and the related guidance set



                                       30
<PAGE>

out in Securities and Exchange Commission Staff Bulletin No. 98, has eliminated
the inclusion of cheap stock from the calculation of basic and diluted earnings
per share prior to issuance of the securities. Accordingly, basic and diluted
earnings per share in 1996 and 1995 have been restated from $(1.39) and $(3.99),
respectively.

Recent Pronouncements

         The FASB recently issued Statement of Accounting Standards No. 130
(SFAS 130) "Reporting Comprehensive Income". This statement requires changes in
comprehensive income to be shown in a financial statement that is displayed with
the same prominence as other financial statements. The Company believes the
implementation of this statement will not have a material impact on the
financial statements.




                                       31
<PAGE>



ITEM 7A.          QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT
                  MARKET RISK

                  None.

ITEM 8.           FINANCIAL STATEMENTS

CUBIST PHARMACEUTICALS, INC.

INDEX TO FINANCIAL STATEMENTS

<TABLE>
<CAPTION>
                                                                                                                        Page
                                                                                                                       ------
<S>                                                                                                                    <C>
        Report of Independent Accountants.............................................................................    33

        Balance Sheets as of December 31, 1997 and 1996...............................................................    34

        Statements of Operations for the years ended December 31, 1997, 1996 and 1995.................................    35

        Statements of Cash Flows for the years ended December 31, 1997, 1996 and 1995.................................    36

        Statements of Changes in Stockholders' Equity for the years ended December 31, 1997, 1996 and 1995............    37

        Notes to Financial Statements.................................................................................    40
</TABLE>



                                       32
<PAGE>

REPORT OF INDEPENDENT ACCOUNTANTS

To the Board of Directors and Stockholders of
Cubist Pharmaceuticals, Inc.:

         We have audited the accompanying balance sheets of Cubist
Pharmaceuticals, Inc. as of December 31, 1997 and 1996, and the related
statements of operations, changes in stockholders' equity, and cash flows for
each of the three years in the period ended December 31, 1997. These financial
statements are the responsibility of the Company's management. Our
responsibility is to express an opinion on these financial statements based on
our audits.

         We conducted our audits in accordance with generally accepted auditing
standards. Those standards require that we plan and perform the audit to obtain
reasonable assurance about whether the financial statements are free of material
misstatement. An audit includes examining, on a test basis, evidence supporting
the amounts and disclosures in the financial statements. An audit also includes
assessing the accounting principles used and significant estimates made by
management, as well as evaluating the overall financial statement presentation.
We believe that our audits provide a reasonable basis for our opinion.

         In our opinion, the financial statements referred to above present
fairly, in all material respects, the financial position of Cubist
Pharmaceuticals, Inc. as of December 31, 1997 and 1996, and the results of its
operations and its cash flows for each of the three years in the period ended
December 31, 1997 in conformity with generally accepted accounting principles.


Boston, Massachusetts                                  COOPERS & LYBRAND L.L.P.
January 19, 1998



                                       33
<PAGE>

CUBIST PHARMACEUTICALS, INC.

BALANCE SHEETS

<TABLE>
<CAPTION>
                                                                     December 31,
                                                            ----------------------------
                                                                1997            1996
                                                            ------------    ------------
<S>                                                         <C>             <C>         
ASSETS
Current Assets:
         Cash and cash equivalents ......................   $  2,837,600    $ 19,329,353
         Short-term investments .........................      6,709,623            --
         Accounts receivable ............................         53,333         505,267
         Prepaid expenses and other current assets ......        142,635         286,642
                                                            ------------    ------------
         Total current assets ...........................      9,743,191      20,121,262
Property and equipment ..................................      5,893,101       4,898,538
         Less: Accumulated depreciation and
              amortization ..............................     (2,712,341)     (1,741,152)
                                                            ------------    ------------
         Property and equipment, net ....................      3,180,760       3,157,386
Long-term investments ...................................      8,569,107            --
Other assets ............................................        180,294         173,799
                                                            ------------    ------------
                  Total assets ..........................   $ 21,673,352    $ 23,452,447
                                                            ------------    ------------
                                                            ------------    ------------
LIABILITIES AND STOCKHOLDERS' EQUITY
Current Liabilities:
         Accounts payable ...............................   $    275,260    $    741,409
         Accrued expenses ...............................        492,304         484,732
         Deferred revenue ...............................           --           126,900
         Current portion of long-term debt ..............        189,730         188,062
         Current portion of capital lease obligations ...        548,351         559,767
                                                            ------------    ------------
                  Total current liabilities .............      1,505,645       2,100,870
Long-term debt, net of current portion ..................        100,072         291,683
Long-term capital lease obligation, net of current
         portion ........................................      1,004,969         761,284
                                                            ------------    ------------
                  Total liabilities .....................      2,610,686       3,153,837
                                                            ------------    ------------
Commitments (Note J)

Stockholders' Equity:
Preferred Stock non-cumulative; convertible, $.001
     par value; authorized 5,000,000 shares, 1997 and
     1996; issued and outstanding 1997 and 1996 no shares           --              --
Common Stock, $.001 par value; authorized
     25,000,000 shares, 1997 and 1996;
     issued and outstanding 1997 10,580,555 shares;
     issued and outstanding 1996 9,544,373 shares .......         10,581           9,544
Additional paid-in capital ..............................     42,047,966      36,019,608
Accumulated deficit .....................................    (22,995,881)    (15,730,542)
                                                            ------------    ------------
                  Total stockholders' equity ............     19,062,666      20,298,610
                                                            ------------    ------------
                  Total liabilities and stockholders'
                  equity ................................   $ 21,673,352    $ 23,452,447
                                                            ------------    ------------
                                                            ------------    ------------
</TABLE>


The accompanying notes are an integral part of the financial statements.



                                       34
<PAGE>

CUBIST PHARMACEUTICALS, INC.

STATEMENTS OF OPERATIONS

<TABLE>
<CAPTION>
                                                           For the Years Ended December 31,
                                                     --------------------------------------------
                                                         1997            1996            1995
                                                     ------------    ------------    ------------ 
<S>                                                  <C>             <C>             <C>         
Sponsored research revenues ......................   $  2,733,083    $  4,985,052    $  1,271,333
Operating expenses:
         Research and development ................      9,340,928       6,871,149       4,964,876
         General and administrative ..............      3,292,241       1,989,284       1,708,513
                                                     ------------    ------------    ------------ 
                  Total operating expenses .......     12,633,169       8,860,433       6,673,389
Interest income ..................................      1,038,532         306,017         239,030
Interest expense .................................       (237,119)       (229,305)       (232,980)
Other income (Note E) ............................      1,833,334            --              --
                                                     ------------    ------------    ------------ 
         Net loss ................................   $ (7,265,339)   $ (3,798,669)   $ (5,396,006)
                                                     ------------    ------------    ------------ 
                                                     ------------    ------------    ------------ 
Basic and diluted net loss per common share ......   $      (0.73)   $      (1.49)   $      (5.47)
                                                     ------------    ------------    ------------ 
                                                     ------------    ------------    ------------ 
Weighted average number of common shares for basic
 and diluted net loss per common share ...........      9,994,718       2,553,999         986,255
                                                     ------------    ------------    ------------ 
                                                     ------------    ------------    ------------ 
</TABLE>


The accompanying notes are an integral part of the financial statements.



                                       35
<PAGE>

CUBIST PHARMACEUTICALS, INC.

STATEMENTS OF CASH FLOWS

<TABLE>
<CAPTION>
                                                                  For the Years Ended December 31,
                                                           --------------------------------------------
                                                                1997           1996            1995
                                                           ------------    ------------    ------------ 
<S>                                                        <C>             <C>             <C>          
Cash flows for operating activities:
     Net loss ..........................................   $ (7,265,339)   $ (3,798,669)   $ (5,396,006)
     Adjustments to reconcile net loss to net cash
      used in operating activities:
        Gain on sale of equity interest ................     (1,833,334)           --              --
        Amortization of equity interest ................        833,334            --              --
         Depreciation and amortization .................      1,057,887         740,408         570,556
         Changes in assets and liabilities:
              Accounts receivable ......................        451,934         482,733        (988,000)
              Prepaid expenses and other current assets         144,007        (219,646)         15,713
              Other assets .............................         (6,495)        (15,228)         (8,390)
              Accounts payable and accrued expenses ....       (458,577)        911,622        (708,104)
              Deferred revenue .........................       (126,900)        126,900            --
                                                           ------------    ------------    ------------ 
                  Total adjustments ....................         61,856       2,026,789      (1,118,225)
                                                           ------------    ------------    ------------ 
Net cash used for operating activities .................     (7,203,483)     (1,771,880)     (6,514,231)
                                                           ------------    ------------    ------------ 
Cash flows for investing activities:
     Purchase of equipment .............................       (899,810)       (640,329)           --
     Leasehold improvements ............................        (94,753)       (423,256)        (99,325)
     Purchase of equity interest .......................     (1,000,000)           --              --
     Proceeds from sale of equity interest .............      2,000,000            --              --
     Purchase of short-term investments ................    (22,686,443)           --        (3,942,610)
     Redemption and maturities of short-term investments     15,976,820       1,006,569       2,936,041
     Purchase of long-term investments .................     (8,569,107)           --              --
                                                           ------------    ------------    ------------ 
Net cash used for investing activities .................    (15,273,293)        (57,016)     (1,105,894)
                                                           ------------    ------------    ------------ 
Cash flows from financing activities:
     Issuance of stock .................................      5,942,697      19,146,448       8,467,928
     Proceeds from long-term debt ......................           --              --           345,500
     Repayments of long-term debt ......................       (189,943)       (168,565)       (141,130)
     Proceeds from capital lease financing .............        927,686         599,593          94,671
     Principal payments of capital lease obligations ...       (695,417)       (468,782)       (318,272)
                                                           ------------    ------------    ------------ 
Net cash provided by financing activities ..............      5,985,023      19,108,694       8,448,697
                                                           ------------    ------------    ------------ 
Net increase (decrease) in cash and cash equivalents ...    (16,491,753)     17,279,798         828,572
Cash and cash equivalents at beginning of year .........     19,329,353       2,049,555       1,220,983
                                                           ------------    ------------    ------------ 
Cash and cash equivalents at end of year ...............   $  2,837,600    $ 19,329,353    $  2,049,555
                                                           ------------    ------------    ------------ 
                                                           ------------    ------------    ------------ 
Supplemental disclosures of cash flow information:
     Cash paid during the year for interest ............   $    237,119    $    229,305    $    232,980
</TABLE>


The accompanying notes are an integral part of the financial statements.



                                       36
<PAGE>

CUBIST PHARMACEUTICALS, INC.
STATEMENTS OF CHANGES IN STOCKHOLDERS' EQUITY

For the Years Ended December 31, 1997, 1996 and 1995

<TABLE>
<CAPTION>
                                                                                                                            
                                                                                                                            
                                                                                                                            
                                # of Shares     # of Shares      # of Shares     # of Shares     # of Shares  $             
                                Preferred A     Preferred B      Preferred C     Preferred D       Common     Preferred     
                                -----------     -----------      -----------     -----------     -----------  -----------   
<S>                             <C>             <C>              <C>             <C>             <C>          <C>
12/31/94 Balance ..........      5,000,000      14,733,370            --              --           910,027   $     19,733   
                                 ---------      ----------                                         -------   ------------   
                                 ---------      ----------                                         -------   ------------   
Series C Preferred Stock
    par $.001 at $.60 share                                       15,017,813                                 $     15,018   
Series C Preferred Stock
    Offering Expenses .....                                                                                                 
Common Stock par $.007
    at $.35 and $.42 share                                                                         114,082                  
Exercise of Common Stock
    Options ...............                                                                            785                  
Repurchase of Common
    Stock .................                                                                         (8,232)                 
Repayment of Notes
    Receivable Preferred
    Series B ..............                                                                                                 
Notes Receivable Common
    Stock .................                                                                                                 
Forgiveness of Promissory
    Notes .................                                                                                                 
Issuance of Stock
    Options ...............                                                                                                 
Amortization of Deferred
    Compensation ..........                                                                                                 
Net Loss ..................                                                                                                 
                                 ---------      ----------      ----------                       ---------   ------------   
12/31/95 Balance ..........      5,000,000      14,733,370      15,017,813            --         1,016,662   $     34,751   
                                 ---------      ----------      ----------                       ---------   ------------   
                                 ---------      ----------      ----------                       ---------   ------------   
</TABLE>

<TABLE>
<CAPTION>
                                                 $                                                                            
                                                 Additional Paid-in Capital                    $               $              
                                                 ------------------------------------------                                   
                                  $              Issuance of    Notes          Deferred        Accumulated     Stockholders'  
                                  Common         Shares         Receivable     Compensation    Deficit         Equity         
                                  -----------   ------------   ------------    ------------    ------------    ------------   
<S>                              <C>            <C>            <C>             <C>             <C>             <C>
12/31/94 Balance ..........      $        910   $  7,981,632   $   (632,527)   $    (11,030)   $ (6,535,867)   $    822,851   
                                 ------------   ------------   ------------    ------------    ------------    ------------   
                                 ------------   ------------   ------------    ------------    ------------    ------------   
Series C Preferred Stock                                                                                                
    par $.001 at $.60 share                        8,995,670                                                      9,010,688   
Series C Preferred Stock                                                                                                
    Offering Expenses .....                          (45,787)                                                       (45,787)  
Common Stock par $.007                                                                                                  
    at $.35 and $.42 share                114         47,274                                                         47,388   
Exercise of Common Stock                                                                                                
    Options ...............                 1            274                                                            275   
Repurchase of Common                                                                                                    
    Stock .................                (8)        (2,873)                                                        (2,881)  
Repayment of Notes                                                                                                      
    Receivable Preferred                                                                                                
    Series B ..............                                         435,000                                         435,000   
Notes Receivable Common                                                                                                 
    Stock .................                                          (4,989)                                         (4,989)  
Forgiveness of Promissory                                                                                               
    Notes .................                                          23,615                                          23,615   
Issuance of Stock                                                                                                       
    Options ...............                           28,020                        (28,020)                                  
Amortization of Deferred                                                                                                
    Compensation ..........                                                           4,619                           4,619   
Net Loss ..................                                                                      (5,396,006)     (5,396,006)  
                                 ------------   ------------   ------------    ------------    ------------    ------------   
12/31/95 Balance ..........      $      1,017   $ 17,004,210   $   (178,901)   $    (34,431)   $(11,931,873)   $  4,894,773   
                                 ------------   ------------   ------------    ------------    ------------    ------------   
                                 ------------   ------------   ------------    ------------    ------------    ------------   
</TABLE>

The accompanying notes are an integral part of the financial statements.



                                       37
<PAGE>

CUBIST PHARMACEUTICALS, INC.

STATEMENTS OF CHANGES IN STOCKHOLDERS' EQUITY (CONTINUED)

For the Years Ended December 31, 1997, 1996 and 1995

<TABLE>
<CAPTION>
                                                                                                                            
                                                                                                                            
                                                                                                                            
                                # of Shares     # of Shares      # of Shares     # of Shares     # of Shares  $             
                                Preferred A     Preferred B      Preferred C     Preferred D       Common     Preferred     
                                -----------     -----------      -----------     -----------     -----------  -----------   
<S>                             <C>             <C>              <C>             <C>             <C>          <C>
Series D Preferred Stock par
 $.001 at $1.42 share,  net
 of expenses ................                                                      2,816,902                       2,817
Conversion of Preferred Stock
   to Common Stock par $.001    (5,000,000)    (14,733,370)      (15,017,813)     (2,816,902)      5,366,849     (37,568)
Exercise of Stock Options ...                                                                         58,244
Repurchase of Common
    Stock ...................                                                                        (36,634)
Initial Public Offering, net
 of expenses ................                                                                      3,139,252
Forgiveness of Promissory
    Notes ...................
Issuance of Common Stock
   Options and Warrants .....
Amortization of Deferred
    Compensation ............
Net Loss ....................
                                                                                                   ---------             
12/31/96 Balance ............        --            --                --               --           9,544,373           --
                                                                                                   ---------             
                                                                                                   ---------             
</TABLE>

<TABLE>
<CAPTION>
                                                 $                                                                            
                                                 Additional Paid-in Capital                    $               $              
                                                 ------------------------------------------                                   
                                  $              Issuance of    Notes          Deferred        Accumulated     Stockholders'  
                                  Common         Shares         Receivable     Compensation    Deficit         Equity         
                                  -----------   ------------   ------------    ------------    ------------    ------------   
<S>                              <C>            <C>            <C>             <C>             <C>             <C>
Series D Preferred Stock par 
 $.001 at $1.42 share,  net  
 of expenses ................                      3,941,727                                                     3,944,544
Conversion of Preferred Stock
   to Common Stock par $.001          5,367           32,201                                                             0
Exercise of Stock Options ...            58           35,232                                                        35,290
Repurchase of Common         
    Stock ...................           (37)         (12,273)                                                      (12,310)
Initial Public Offering, net 
 of expenses ................         3,139       15,151,343                                                    15,154,482
Forgiveness of Promissory    
    Notes ...................                                       24,442                                          24,442
Issuance of Common Stock     
   Options and Warrants .....                        101,378                      (101,378)                              0
Amortization of Deferred     
    Compensation ............                                                       56,058                          56,058
Net Loss ....................                                                                   (3,798,669)     (3,798,669)
                                -----------     ------------   -----------    ------------    ------------    ------------
12/31/96 Balance ............   $     9,544     $ 36,253,818   $  (154,459)   $    (79,751)   $(15,730,542)   $ 20,298,610
                                -----------     ------------   -----------    ------------    ------------    ------------
                                -----------     ------------   -----------    ------------    ------------    ------------
</TABLE>


The accompanying notes are an integral part of the financial statements.



                                       38
<PAGE>

CUBIST PHARMACEUTICALS, INC.

STATEMENTS OF CHANGES IN STOCKHOLDERS' EQUITY (CONTINUED)

For the Years Ended December 31, 1997, 1996 and 1995

<TABLE>
<CAPTION>
                                                                                                                            
                                                                                                                            
                                                                                                                            
                                # of Shares     # of Shares      # of Shares     # of Shares     # of Shares  $             
                                Preferred A     Preferred B      Preferred C     Preferred D       Common     Preferred     
                                -----------     -----------      -----------     -----------     -----------  -----------   
<S>                             <C>             <C>              <C>             <C>             <C>          <C>
Exercise of Stock Option                                                                             57,981
Repurchase of Common
 Stock ..................                                                                            (1,390)
Issuance of Common Stock,
 net of offering expenses                                                                           979,591
Amortization of Deferred
 Compensation ...........
Forgiveness of
 Promissory  Notes ......
Net Loss ................
                                                                                                  ----------          
12/31/97 Balance ........           --               --              --               --          10,580,555        --
                                                                                                  ----------          
                                                                                                  ----------          
</TABLE>

<TABLE>
<CAPTION>
                                                 $                                                                            
                                                 Additional Paid-in Capital                    $               $              
                                                 ------------------------------------------                                   
                                  $              Issuance of    Notes          Deferred        Accumulated     Stockholders'  
                                  Common         Shares         Receivable     Compensation    Deficit         Equity         
                                  -----------   ------------   ------------    ------------    ------------    ------------   
<S>                              <C>            <C>            <C>             <C>             <C>             <C>
Exercise of Stock Option         $         58   $    119,320                                                   $    119,378
Repurchase of Common      
 Stock ..................                  (1)          (519)                                                          (520)
Issuance of Common Stock, 
 net of offering expenses                 980      5,902,859       (80,000)                                       5,823,839
Amortization of Deferred  
 Compensation ...........                                           20,000           43,924                          63,924
Forgiveness of            
 Promissory  Notes ......                                           22,774                                           22,774
Net Loss ................                                                                        (7,265,339)     (7,265,339)
                                 ------------   ------------   -----------      -----------    ------------    ------------
12/31/97 Balance ........        $     10,581   $ 42,275,478   $  (191,685)     $   (35,827)   $(22,995,881)   $ 19,062,666
                                 ------------   ------------   -----------      -----------    ------------    ------------
                                 ------------   ------------   -----------      -----------    ------------    ------------
</TABLE>


The accompanying notes are an integral part of the financial statements.



                                       39
<PAGE>

CUBIST PHARMACEUTICALS, INC.

NOTES TO FINANCIAL STATEMENTS

A. Nature of Business

         Cubist Pharmaceuticals, Inc. ("Cubist" or the "Company") is a
biopharmaceutical company founded in May 1992 and is engaged in the research,
development and commercialization of novel classes of antiinfective drugs to
treat infectious diseases caused by bacteria and fungi, primarily those
resistant to existing antiinfective drugs. Cubist has established multiple
technology licenses and collaborations, has established a network of advisors
and collaborators and is located in Cambridge, Massachusetts.

B. Accounting Policies

     Basis of Presentation

         The accompanying financial statements are stated on an accrual basis.

     Use of Estimates

         The preparation of financial statements in conformity with generally
accepted accounting principles requires management to make certain estimates and
assumptions that affect the reported amounts of assets and liabilities, and
disclosure of contingent assets and liabilities at the date of the financial
statements and the reported amounts of revenues and expenses during the reported
period. Actual results could differ from those estimates.

     Risks and Uncertainties

         The Company is subject to risks common to companies in the
biotechnology industry including, but not limited to, development by its
competitors of new technological innovations, dependence on key personnel,
protection of proprietary technology, and compliance with FDA government
regulations.

     Cash Equivalents

         Cash equivalents consist of short-term interest-bearing instruments
(U.S. Government treasuries and money market accounts) with original maturities
of three months or less. These investments are carried at cost which
approximates market value.

     Short-term Investments

         Short-term investments, with an original maturity of more than three
months and less than one year when purchased, consisted of certificates of
deposit and investment-grade commercial paper at December 31, 1997. Short-term
investments, all of which are held to maturity, are stated at amortized cost
plus accrued interest, which approximates market value.

     Long-Term Investments

         Long-term investments, with a maturity of more than twelve months when
purchased, consisted of investment-grade corporate debt at December 31, 1997.
Long-term investments, all of which are held to maturity, are stated at
amortized cost plus accrued interest, which approximates market value.



                                       40
<PAGE>

CUBIST PHARMACEUTICALS, INC.

NOTES TO FINANCIAL STATEMENTS (CONTINUED)

B. Accounting Policies (Continued)

Property and Equipment

         Property and equipment are recorded at cost. Depreciation is provided
using the straight-line method over the estimated useful lives of the related
assets, generally three years for computer equipment and five years for
laboratory equipment, furniture and fixtures. Leasehold improvements are stated
at cost and are amortized over the lesser of the life of the lease or their
estimated useful lives. The leasehold improvements are also utilized as
collateral up to a value of $289,802, which relates to the balance of long-term
debt. Maintenance and repairs are charged to expense as incurred, while major
betterments are capitalized. When assets are retired or otherwise disposed of,
the assets and related allowances for depreciation and amortization are
eliminated from the accounts and any resulting gain or loss is reflected in
income.

     Research and Development

         All research and development costs are expensed as incurred.

     Income Taxes

         Research and experimentation and other tax credits, when utilized, will
be recorded using the flow-through method of accounting as a reduction of the
current provision for federal and state income taxes.

     Earnings Per Share

         Effective December 31, 1997, the Company adopted Statement of Financial
Accounting Standards No. 128 (SFAS 128) "Earnings Per Share", which requires the
disclosure of Basic Earnings per Common Share and Diluted Earnings per Common
Share for all periods presented. At December 31, 1997, the Company had 802,468
options and 86,619 warrants outstanding. Adoption of this statement has not
affected the amounts presented in any period because the effect of including
these equity instruments would be anti-dilutive.

         Prior to the adoption of this statement, all common and common
equivalent shares issued during the twelve month period prior to the filing of
the initial public offering ("cheap stock") were included in the calculation of
basic and diluted earnings per share as if they were outstanding for all periods
presented. Adoption of this statement, and the related guidance set out in
Securities and Exchange Commission Staff Accounting Bulletin No. 98, has
eliminated the inclusion of cheap stock from the calculation of basic and
diluted earnings per share prior to issuance of the securities. Accordingly,
basic and diluted earnings per share in 1996 and 1995 have been restated from
$(1.39) and $(3.99), respectively.

C. Property and Equipment

     At December 31, property and equipment consisted of:

<TABLE>
<CAPTION>
                                                         1997           1996
                                                     -----------    -----------
<S>                                                  <C>            <C>        
    Leasehold improvements .......................   $ 2,584,489    $ 2,489,736
    Laboratory equipment .........................     2,389,683      1,799,587
    Furniture and fixtures .......................       286,197        251,427
    Computer equipment ...........................       632,732        357,788
                                                     -----------    -----------
                                                       5,893,101      4,898,538
                                                     -----------    -----------
    Less accumulated depreciation and amortization    (2,712,341)    (1,741,152)
                                                     -----------    -----------
    Property and equipment, net ..................   $ 3,180,760    $ 3,157,386
                                                     -----------    -----------
                                                     -----------    -----------
</TABLE>

Depreciation and amortization expense was $971,189, $659,908 and $542,322 in
1997, 1996 and 1995, respectively.



                                       41
<PAGE>

CUBIST PHARMACEUTICALS, INC.

NOTES TO FINANCIAL STATEMENTS (CONTINUED)

D. Accrued Expenses

         At December 31, accrued expenses consisted of:

<TABLE>
<CAPTION>
                                                1997       1996
                                              --------   --------
<S>                                           <C>        <C>     
Payroll and benefits ......................   $218,583   $125,087
Vacation ..................................     67,837     60,019
Construction ..............................       --       46,250
Legal, audit and patent ...................    119,500     68,275
Database ..................................       --       42,200
Annual report .............................     35,000     60,000
Utilities .................................       --       76,339
Miscellaneous .............................     51,384      6,562
                                              --------   --------
Total accrued expenses ....................   $492,304   $484,732
                                              --------   --------
                                              --------   --------
</TABLE>


E. Collaborative Research Agreements

         On December 15, 1995, the Company entered into a collaborative research
agreement with Pfizer, Inc. Under the terms of the agreement, Pfizer paid the
Company a technology licensing fee upon execution and research support payments.
These payments were recognized as income under the terms of the agreement. In
addition, Pfizer reimbursed the Company for expenses related to the screening of
Pfizer compounds against the Company's targets. In accordance with the
agreement, these payments were recognized as revenue as the work was completed.
The Company included in sponsored research revenues $150,000, $587,000 and
$988,000 in 1997, 1996 and 1995, respectively. On June 20, 1997, the Company's
collaborative agreement with Pfizer expired pursuant to its own terms. Prior to
such expiration, the Company had received all of the research support payments
and technology licensing fees that the Company was entitled to receive under
that collaborative agreement. In accordance with the terms of that collaborative
agreement, the Company selected and licensed from Pfizer one of the chemical
compounds that was identified and characterized during the Company's
collaboration with Pfizer. Pursuant to the terms of that license, the Company
may develop and commercialize such licensed compound without further obligation
to Pfizer.

         In June 1996, the Company entered into a collaborative research
agreement with Bristol-Myers Squibb Company ("Bristol-Myers Squibb"). Under the
terms of the agreement, Bristol-Myers Squibb purchased from the Company
$4,000,000 of the Company's Preferred Stock upon execution of the agreement, and
has agreed to make payments to the Company upon the achievement of certain
milestones. These milestone payments are recognized as income as earned under
the terms of the agreement. In addition, Bristol-Myers Squibb will reimburse the
Company a fixed amount for research and development expenses relating to the
production of certain targets and also for expenses relating to the screening of
Bristol-Myers Squibb compounds against the Company's targets over three years,
with an option to fund a fourth year. These reimbursements are to be paid at the
beginning of each calendar quarter in accordance with the agreement. The Company
included in sponsored research revenues $500,000 and $1,000,000 in milestone
payments in 1997 and 1996, respectively; and $1,000,000 and $516,668 in 1997 and
1996, respectively, for certain research and development revenues in accordance
with the agreement.



                                       42
<PAGE>

CUBIST PHARMACEUTICALS, INC.

NOTES TO FINANCIAL STATEMENTS (CONTINUED)

E. Collaborative Research Agreements (Continued)

         In June 1996, the Company entered into a collaborative research
agreement with Merck & Co., Inc. ("Merck"). Under the terms of the agreement,
Merck paid the Company a technology licensing fee upon execution and will pay
certain milestone payments. These payments are recognized as income as earned
under the terms of the agreement. In addition, Merck will reimburse the Company
for research and development expenses relating to the production of certain
targets; for expenses relating to the screening of Merck compounds against the
Company's targets; and for expenses relating to compound optimization. These
payments are recognized as revenue as the work is completed. During 1996, the
Company included in sponsored research revenues $1,500,000 for the technology
licensing fee and $875,233 and $1,012,300 in 1997 and 1996, respectively, for
certain research and development revenues in accordance with the agreement.

         In May 1997, the Company acquired 333,333 shares of Series B
Convertible Preferred Stock of Novalon Pharmaceutical Corporation ("Novalon"),
together with an option to purchase all of the capital stock of Novalon. The
aggregate purchase price for such shares and such option was $1.0 million. The
Company allocated all of the $1.0 million aggregate purchase price to the option
based on management's estimates of the relative fair values of the option and
the shares of Series B Convertible Preferred Stock acquired. The value of the
option was amortized over the option period resulting in an $833,333 research
and development expense. On September 29, 1997, the Company agreed to terminate
its option to acquire Novalon and sold its equity position back to Novalon for
$2.0 million resulting in a gain of $1,833,333 included in other income. In 
connection with this transaction, the Company, at its sole discretion, was
granted a one year option to purchase up to twenty percent of the outstanding
shares of Novalon from existing shareholders at $6.00 per share payable in cash.
The Company will pay Novalon a percent of revenues received by the Company that
relates to the use of the technology and currently pays a monthly fee for
research funding to Novalon.

F. License Agreement

         On November 7, 1997, the Company entered into a license agreement with
Eli Lilly and Company ("Eli Lilly") pursuant to which the Company acquired
exclusive worldwide rights to develop, manufacture and market daptomycin.
Daptomycin is a natural product being developed for the treatment of
Staphylococcus aureus and enterococcus infections. In exchange for such license,
the Company has paid an upfront license fee in cash and, if certain drug
development milestones are achieved, has agreed to pay milestone payments by
issuing shares of Common Stock to Eli Lilly. In addition, the Company will be
required to pay royalties to Eli Lilly on worldwide sales of daptomycin.

G. Financing

         On July 18, 1997, the Company completed a private equity financing in
which the Company raised $6.0 million before offering expenses of $96,161 by
issuing 979,591 common shares at $6.125 per share. These shares were
subsequently registered with the Securities and Exchange Commission.



                                       43
<PAGE>

CUBIST PHARMACEUTICALS, INC.

NOTES TO FINANCIAL STATEMENTS (CONTINUED)

H. Stockholders' Equity

     Common Stock

         As of December 31, 1997, 1,095,388 shares of Common Stock were issued
to employees, scientific founders and consultants of the Company. At December
31, 1997, 43,514 of these shares issued are subject to repurchase, at the
Company's option, at the original issuance price in accordance with vesting
provisions upon termination of the shareholder's relationship with the Company.

     Warrants

         Total warrants outstanding at December 31, 1997 were 86,619. On October
23, 1996, the Company amended 17,142 of these warrants issued to both Drs. Rebek
and Schimmel in May 1995 to extend the expiration date of such warrants from the
effective date of the Company's initial public offering to May 15, 2005, and to
provide that the warrants will vest in four equal annual installments commencing
upon the first anniversary of their grant date. As a result of this amendment,
the Company recorded deferred compensation in the amount of $62,000 to be
amortized to the income statement over the remaining vesting period from October
1996 to May 1999.

     Notes Receivable from Related Parties

         The Company has accepted a promissory note from the Chief Executive
Officer in consideration for the Preferred Stock issued to him. The aggregate
principal amount of this note at December 31, 1997 is $131,685 and is reflected
in stockholders' equity as a reduction to paid-in capital. In 1997, the term of
this note was extended to fall due in equal quarterly installments of $10,000
commencing on March 31, 1998.

         The Company has accepted a promissory note from the Chief Business
Officer in consideration for the Common Stock options issued to him. The
aggregate principal amount of this note at December 31, 1997 is $80,000 and is
reflected in stockholders' equity as a reduction to paid-in-capital. This note
has an annual interest rate of 4% and falls due May 19, 2000. The note will be
forgiven in three equal annual installments, contingent upon the Chief Business
Officer's employment, from May 1998 to May 2000.


I. Stock Options

         The Company has a stock option plan under which options to purchase
1,500,000 shares of its Common Stock may be granted to employees, directors,
officers or consultants. The options are granted at fair market value on the
date of the grant as determined by the Board of Directors, vest ratably over a
four-year period and expire ten years from the date of grant. In addition, the
Company issued to certain consultants and directors non-qualified stock options
to purchase 87,300 shares of its Common Stock. During 1995 and 1994, the Company
allowed employees and consultants to exercise their full grants to take
advantage of certain favorable tax benefits. The Company reserved the right to
repurchase any unearned shares at the original purchase price if the employee or
consultant does not fulfill their vesting requirement. 1,390, 36,634 and 8,232
shares of previously exercised options were repurchased in 1997, 1996 and 1995,
respectively, because vesting schedules were not fulfilled.

         The Company adopted the disclosure provisions of SFAS 123, Accounting
for Stock Based Compensation, in 1996 and has applied APB Opinion 25 and related
Interpretations in accounting for its plans. Had compensation costs for the
Company's stock-based compensation plan been determined based on the fair value
at the grant dates as calculated in accordance with SFAS 123, the Company's net
loss and loss per share for the years ended December 31, 1997, 1996 and 1995
would have been increased to the pro forma amounts indicated below:



                                       44
<PAGE>

CUBIST PHARMACEUTICALS, INC.

NOTES TO FINANCIAL STATEMENTS (CONTINUED)

I. Stock Options (Continued)

<TABLE>
<CAPTION>
                     1997                                1996                                 1995
                                      Basic and Diluted                   Basic and Diluted                    Basic and Diluted
                     Net Loss         Loss Per Share     Net Loss         Loss Per Share      Net Loss         Loss Per Share
                     -----------      -----------------  -----------      -----------------   -----------      -----------------
<S>                  <C>              <C>                <C>              <C>                 <C>              <C>      
As Reported          $(7,265,339)     $  (0.73)          $(3,798,669)     $  (1.49)           $(5,396,006)     $  (5.47)
Pro forma            $(7,859,006)     $  (0.79)          $(4,053,670)     $  (1.59)           $(5,408,006)     $  (5.48)
</TABLE>


         The fair value of each stock option was estimated on the date of grant
using Black-Scholes option-pricing model with the following weighted-average
assumptions: an expected life of four (4) years, expected volatility of 87%, a
dividend yield of 0% and a risk-free interest rate of 6.36%. The effects of
applying SFAS 123 in this pro forma disclosure are not indicative of future
amounts. Additional awards in future years are anticipated.

         A summary of the status of the Company's stock option plan as of
December 31, 1997, 1996, 1995 and changes during each of the years then ended,
is presented below:

<TABLE>
<CAPTION>
                                                              1997                    1996                    1995
                                                                         WAEP*                   WAEP*                   WAEP*
                                                              Number     per share    Number     per share    Number     per share
                                                              -------    ---------    -------    ---------    -------    ---------
<S>                                                           <C>        <C>          <C>        <C>          <C>        <C>    
Balance at January 1 .....................................    500,760     $   1.93    159,057     $    .40     42,214     $   .24

Granted ..................................................    438,614         7.06    414,103         2.52    121,442         .42
Exercised ................................................     56,591         2.06     21,610          .61        785         .35
Canceled .................................................     80,315         2.29     50,790          .97      3,814         .35

Balance at December 31 ...................................    802,468     $   4.69    500,760     $   1.93    159,057     $   .40
                                                              -------     --------    -------     --------    -------     -------
Options exercisable at
December 31 ..............................................    191,911     $   2.73     86,560     $   1.19     25,617     $   .26
                                                              -------     --------    -------     --------    -------     -------
                                                              -------     --------    -------     --------    -------     -------
Weighted  average  grant-date fair value of 
options granted during the year ..........................          $   5.41                 $  2.52               $   .42
</TABLE>

- -------------------------------------------
*  Weighted-Average Exercise Price

The following table summarizes information about stock options outstanding at
December 31, 1997:

<TABLE>
<CAPTION>
                    Options Outstanding                                   Options Exercisable
                    ---------------------------------------------------   -------------------------------
Range of            Number         Remaining           Weighted-Average   Number         Weighted-Average
Exercise Prices     Outstanding    Contractual Life    Exercise Price     Exercisable    Exercise Price
- ---------------     -----------    ----------------    ----------------   -----------    ----------------
<C>                 <C>            <C>                 <C>                <C>            <C>     
$.007 - $1.96       333,263        8.1 years           $   1.45           145,966        $   1.29
$5.25 - $7.00       247,905        9.6 years               6.04            18,344            6.13
$8.00 - $10.125     221,300        9.3 years               8.03            27,601            8.04
                    -------        ---------           --------           -------        --------
                    802,468        8.9 years           $   4.69           191,911        $   2.73
                    -------        ---------           --------           -------        --------
                    -------        ---------           --------           -------        --------
</TABLE>


J. Lease Commitments

         The Company leases its facilities under an operating lease agreement
which expires on September 15, 2003 and is renewable at the Company's option for
one additional five-year period. Under the terms of the lease, the Company is
obligated to pay its prorated share of common operating expenses and real estate
taxes as well as base rents. In addition, the Company entered into an agreement
with the landlord under which the landlord provided financing to the Company for
a portion of the buildout cost ($543,393) at an interest rate of 12% per year
payable in equal monthly installments of $12,087 over five years through October
1998. At December 31, 1997, the outstanding principal balance was $114,484. The
Company also provided a security deposit of $100,000 upon execution of the
lease. The security deposit bears interest in a segregated account,

CUBIST PHARMACEUTICALS, INC.

NOTES TO FINANCIAL STATEMENTS (CONTINUED)

J. Lease Commitments (Continued)



                                       45
<PAGE>

and is partially refundable ($79,000 plus interest) upon the fifth anniversary,
and fully refundable plus interest within thirty days after the expiration of
the lease, provided no event of default has occurred. The Company also financed
an additional $345,500 during the first quarter of 1995 relating to a 6,510
square foot facility expansion completed during the first week of January 1995.
This additional debt is payable in equal monthly installments of $7,685 over
five years with an annual interest rate of 12% through February 2000. No
additional security deposit was required. At December 31, 1997, the outstanding
principal balance was $175,318.

         The Company leases certain equipment under long-term capital leases.
The cost of this equipment included in fixed assets was $3,279,151 at the end of
1997 and $2,320,201 at the end of 1996, with associated accumulated depreciation
of $1,803,995 at December 31, 1997 and $1,042,297 at December 31, 1996. The
Company has an option to purchase all of the lease equipment at a price to be
negotiated at lease end. Future lease payments for non-cancelable leases for the
respective years ended December 31 are as follows:

<TABLE>
<CAPTION>
                                                    Operating Leases      Capital Leases
                                                    ----------------      --------------
<S>                                                 <C>                   <C>       
         1998 ............................          $   171,365           $  685,135
         1999 ............................              192,364              563,083
         2000 ............................              207,679              406,383
         2001 ............................              207,679              145,598
         2002 ............................              207,679                 --
         2003 and thereafter .............              164,413                 --
                                                    -----------           ----------
Total minimum lease payments .............          $ 1,151,179           $1,800,199
                                                    -----------           ----------
Less amount representing interest payments                                  (246,879)
                                                                         -----------
Present value of minimum lease payments ..                                 1,553,320
Less current portion .....................                                  (548,351)
                                                                         -----------
Long-term obligation .....................                               $ 1,004,969
                                                                         -----------
                                                                         -----------
</TABLE>

         Lease payments under operating leases were $246,498 in fiscal year
1997, $248,784 in fiscal year 1996, and $207,898 in fiscal year 1995.

K. Employee Benefits

         The Company instituted a 401(k) savings plan in 1993, in which
substantially all of its permanent employees are eligible to participate.
Participants may contribute up to 15% of their annual compensation to the plan,
subject to certain limitations. The Company contributes a matching amount of up
to 1.5% of a participant's total compensation or $500 annually, whichever is
less. The Company contributed $20,165, $16,025 and $14,072, during 1997, 1996
and 1995 respectively.

L. Income Taxes

         The Company follows the liability method of accounting for income taxes
in accordance with the provisions of Statement of Financial Accounting Standards
(SFAS) No. 109, "Accounting for Income Taxes," whereby a deferred tax liability
is measured by the enacted tax rates which will be in effect when any
differences between the financial statements and tax basis of assets reverse.
The deferred tax liability can be reduced by net operating losses being carried
forward for tax purposes.




CUBIST PHARMACEUTICALS, INC.

NOTES TO FINANCIAL STATEMENTS (CONTINUED)

L. Income Taxes (Continued)

                                       46
<PAGE>

         The tax effects of temporary differences that give rise to significant
portions of the deferred tax assets and liabilities are presented below:

<TABLE>
<CAPTION>
                                               1997                   1996
                                              ------------           -----------
<S>                                           <C>                    <C>        
Net operating loss carryforwards ...          $  5,780,000           $ 4,376,000
Capitalized research and development             2,690,000             1,700,000
Research and experimentation credits             1,575,000               765,000
Other, net .........................               377,000               306,000
                                              ------------           -----------
Total Deferred Tax Assets ..........          $ 10,422,000           $ 7,147,000
                                              ------------           -----------
Valuation reserve ..................          $(10,422,000)          $(7,147,000)
                                              ------------           -----------
                                              ------------           -----------
</TABLE>

         The federal and state net operating loss and tax credit carryforwards
begin to expire in the years 2007 and 1997, respectively. Research and
experimentation tax credits of approximately $325,000 begin to expire in 2008.
The net operating loss carryforwards may be subject to an annual limitation as a
result of the change in ownership due to the initial public offering. The
Company has established a valuation reserve against the deferred tax benefit
arising from these carryforwards due to the uncertainty of earning sufficient
taxable income to receive the benefit and accordingly has not given recognition
to these tax benefits in these financial statements. These carryforwards are
also subject to review by the Internal Revenue Service.

M.  Recent Pronouncements

         The FASB recently issued Statement of Accounting Standards No. 130
(SFAS 130) "Reporting Comprehensive Income". This statement requires changes in
comprehensive income to be shown in a financial statement that is displayed with
the same prominence as other financial statements. The Company believes the
implementation of this statement will not have a material impact on the
financial statements.




ITEM 9.           CHANGES IN AND DISAGREEMENTS WITH ACCOUNTANTS ON ACCOUNTING 
                  AND FINANCIAL DISCLOSURE

          None.

PART III



                                       47
<PAGE>

ITEM 10.          DIRECTORS AND EXECUTIVE OFFICERS OF THE REGISTRANT

         Information with respect to Directors and compliance with Section 16(a)
of the Securities Exchange Act may be found in the sections captioned "Proposal
No. 1 - Election of Directors", "Executive Compensation" and "Section 16(a)
Beneficial Ownership Reporting Compliance" appearing in the definitive Proxy
Statement to be delivered to Stockholders in connection with the Annual Meeting
of Stockholders to be held on May 21, 1998. Such information is incorporated
herein by reference. Information with respect to Executive Officers may be found
under the section captioned "Executive Officers of the Registrant" in Part I of
this Annual Report on Form 10-K.

ITEM 11.          EXECUTIVE COMPENSATION

         The information required with respect to this item may be found in the
sections captioned "Executive Compensation" appearing in the definitive Proxy
Statement to be delivered to Stockholders in connection with the Annual Meeting
of Stockholders to be held on May 21, 1998. Such information is incorporated
herein by reference.

ITEM 12.          SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT

         The information required with respect to this item may be found in the
section captioned "Principal Stockholders" and "Proposal No. 1 - Election of
Directors" appearing in the definitive Proxy Statement to be delivered to
Stockholders in connection with the Annual Meeting of Stockholders to be held on
May 21, 1998. Such information is incorporated herein by reference.

ITEM 13.          CERTAIN RELATIONSHIPS AND RELATED TRANSACTIONS

         The Information required with respect to this item may be found in the
section captioned "Certain Transactions" appearing in the definitive Proxy
Statement to be delivered to Stockholders in connection with the Annual Meeting
of Stockholders to be held on May 21, 1998. Such information is incorporated
herein by reference.

PART IV

ITEM 14.          EXHIBITS, FINANCIAL STATEMENT SCHEDULES AND REPORTS ON
                  FORM 8-K

(a) Documents Filed as part of Form 10-K

1. Financial Statements.

         The following financial statements and supplementary data are included
in Part II Item 8 filed as part of this report:

   -     Report of Independent Accountants
   -     Balance Sheets as of December 31, 1997 and 1996
   -     Statements of Operations for the years ended 
          December 31, 1997, 1996 and 1995
   -     Statements of Cash Flows for the years ended 
          December 31, 1997, 1996 and 1995
   -     Statements of Stockholders' Equity for the years ended 
          December 31, 1997, 1996 and 1995
   -     Notes to Financial Statements

2. Financial Statement Schedule.

     None.

         Schedules not listed above have been omitted because they are not
applicable, not required or the information required is shown in the financial
statements or the notes thereto.

3. List of Exhibits.

<TABLE>
<CAPTION>

Exhibits
- ---------
<S>      <C>                                                                  
         *3.3     Restated Certificate of Incorporation of the Registrant.
</TABLE>

                                       48
<PAGE>

<TABLE>
<CAPTION>

Exhibits
- ---------
<S>      <C>                                                                  
          *3.1    Restated Certificate of Incorporation of the Registrant.
          *3.2    Amended and Restated By-Laws of the Registrant, as amended to
                  date. 
          *4.1    Specimen certificate for shares of Common Stock.
        +*10.1    Patent License Agreement between the Registrant and the
                  Massachusetts Institute of Technology, dated March 10, 1994.
        +*10.2    License Agreement between the Registrant and the Board
                  of Trustees of Leland Stanford Junior University, dated April
                  1, 1994.
         *10.3    Employment Agreement between the Registrant and Scott M.
                  Rocklage, dated June 20, 1994.
         *10.4    Consulting Agreement between the Registrant and Paul R.
                  Schimmel, dated May 1, 1992.
         *10.5    Amended and Restated 1993 Stock Option Plan.
        +*10.6    Collaborative Research Agreement between the Registrant and
                  Pfizer Inc., dated December 15, 1995.
     **** 10.7    Letter Agreement, dated June 26, 1997, between the
                  Company and Pfizer, Inc.
         *10.8    Collaborative Research and License Agreement between the
                  Registrant and Merck & Co., Inc., dated June 13, 1996.
         *10.9    Collaborative Research and License Agreement between the
                  Registrant and Bristol-Myers Squibb Company and the
                  Registrant, dated June 25, 1996.
        *10.10    Screening Agreement, dated November 28, 1995, between the
                  Registrant and Monsanto Company.
        *10.11    Letter Agreement, dated January 18, 1996, between Pharm-Eco
                  Laboratories, Inc. and the Registrant.
       + 10.12    Research Collaboration and License Agreement with
                  ArQule, Inc., dated October 22, 1997.
        *10.13    Lease Agreement between Registrant and Stimpson Family Trust
                  dated April 30, 1993, regarding 24 Emily Street, Cambridge,
                  MA., as amended by the First Amendment to Lease, dated
                  September 19, 1994. 
        *10.14    Form of Employee Confidentiality and Nondisclosure Agreement.
        *10.15    Master Lease Agreement between the Registrant and Comdisco, 
                  Inc., dated as of August 30, 1993, as amended February 7, 
                  1995, and as further amended on February 26, 1996.
        *10.16    Series B Convertible Preferred Stock Purchase Warrant between
                  the Registrant and Comdisco, Inc., dated August 30, 1993.
        *10.17    Series C Convertible Preferred Stock Purchase Warrants between
                  the Registrant and Comdisco, Inc., dated February 28, 1995 and
                  February 26, 1996.
        *10.18    Series C Convertible Preferred Stock Purchase Options issued
                  to Dr. Paul Schimmel and Dr. Julius Rebek in May 1995, as
                  amended by certain Letter Agreements, dated October 23, 1995,
                  between the Registrant and each of Dr. Schimmel and Dr. Rebek.
        *10.19    Amended and Restated Stockholders Rights Agreement by and
                  among the Registrant and the parties signatory thereto.
       **10.20    Secured Promissory Note, dated as of July 21, 1994, by Scott
                  M. Rocklage to the Registrant.
       **10.21    Amendment to Promissory Note, dated as of July 21, 1996, by
                  and between the Registrant and Scott M. Rocklage.
         10.22    Amendment to Promissory Note, dated as of December 23, 1997,
                  by and between the Registrant and Scott M. Rocklage 
       **10.23    Promissory Note, dated as of October 18, 1995, by and between
                  the Registrant and Scott M. Rocklage.
      **+10.24    Compound Library Screening Agreement between the Registrant
                  and Genzyme Corporation, dated February 24, 1997.
      **+10.25    Library Sample Evaluation Agreement between the Registrant and
                  Pharmacopeia, Inc., dated as of September 11, 1996.
     ****10.26    Stock Purchase Agreement, dated July 18, 1997, between
                  International Biotechnology Trust plc and the Company
     ****10.27    Registration Rights Agreement, dated July 18, 1997, between 
                  International Biotechnology Trust plc and the Company.
     ****10.28    Registration Rights Agreement, dated July 18, 1997, between 
                  each of H&Q Healthcare Investors and H&Q Life Sciences 
                  Investors and the Company.
      ***10.29    Incentive Stock Option Agreement, dated as of May 19, 1997,
                  between Mark Carthy and the Company. 
      ***10.30    Letter Agreement, dated as of May 19, 1997, by Mark Carthy and
                  the Company. 
      ***10.31    Secured Promissory Note, dated May 19, 1997, by Mark Carthy to
                  the Company. 
      ***10.32    Stock Pledge Agreement, dated May 19, 1997, between 
                  Mark Carthy and the Company.
         10.33    Letter Agreement, dated as of January 9, 1998, by Mark Carthy
                  and the Company.
         10.34    Master Lease Agreement between the Registrant and Transamerica
                  Business Credit, dated as of February 14, 1997.
         23.2     Consent of Coopers & Lybrand L.L.P.
         27       Financial Data Schedule

</TABLE>

- --------------------
*    Incorporated by reference from the Company's Registration Statement on Form
     S-1 (Registration No. 333-6795). 
**   Incorporated by reference from the Company's Registration Statement on 
     Form 10K filed with the SEC on March 31, 1997. 
***  Incorporated by reference from the Company's Quarterly Report on 
     Form 10Q filed with the SEC on August 13, 1997.



                                       49
<PAGE>

**** Incorporated by reference from the Company's Registration Statement on Form
     S-1 filed with the SEC on August 18, 1997 (Registration No. 333-33883) as
     amended on Form S-3 filed with the SEC on January 9, 1998. 
+ Confidential Treatment requested as to certain portions.



                                       50
<PAGE>

SIGNATURES

Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange
Act of 1934, the registrant has duly caused this report to be signed on its
behalf by the undersigned, thereunto duly authorized.

                               CUBIST PHARMACEUTICALS, INC.

                              /s/ Scott M. Rocklage
                              -----------------------------------------
                              Scott M. Rocklage
                              President and Chief Executive Officer

Pursuant to the requirements of the Securities Exchange Act of 1934, this report
has been signed below by the following persons on its behalf of the registration
and in the capacities on the dates indicated.

<TABLE>
<CAPTION>

Signature                      Title                                             Date
- ---------                      -----                                             ----
<S>                            <C>                                               <C>
/s/ Scott M. Rocklage                                                            3/12/98
- --------------------------     President, Chief Executive Officer                ------------
    Scott M. Rocklage          and Director
                               (Principal Executive Officer)

/s/ Thomas A. Shea                                                               3/12/98
- --------------------------     Treasurer                                         ------------
    Thomas A. Shea             (Principal Financial and Accounting Officer)


/s/ John K. Clarke                                                               3/12/98
- --------------------------     Chairman of the Board of Directors                ------------
    John K. Clarke


/s/ Barry Bloom                                                                  3/10/98
- --------------------------     Director                                          ------------
    Barry Bloom

/s/ George Conrades                                                              3/10/98
- --------------------------     Director                                          ------------
    George Conrades


/s/ Ellen M. Feeney                                                              3/13/98
- --------------------------     Director                                          ------------
    Ellen M. Feeney


/s/ David W. Martin, Jr.                                                         3/12/98
- --------------------------     Director                                          ------------
    David W. Martin, Jr.


/s/ Terrance G. McGuire                                                          3/13/98
- --------------------------     Director                                          ------------
    Terrance G. McGuire


/s/ Julius Rebek, Jr.                                                            3/10/98
- --------------------------     Director                                          ------------
    Julius Rebek, Jr.


/s/ Paul R. Schimmel                                                             3/13/98
- --------------------------     Director                                          ------------
    Paul R. Schimmel

</TABLE>


                                       51

<PAGE>

                                                                   Exhibit 10.12



                            CONFIDENTIAL TREATMENT
                                       
                 RESEARCH COLLABORATION AND LICENSE AGREEMENT

     This Research Collaboration and License Agreement (this "Agreement") is
entered into as of October 22, 1997 (the "Effective Date") by and between
ArQule, Inc. ("ArQule"), a Delaware corporation, and Cubist Pharmaceuticals,
Inc. ("Cubist"), a Delaware corporation.

                                   RECITALS

     WHEREAS, ArQule and Cubist previously entered into a Material Transfer and
Screening Agreement dated June 4, 1996 (the "MTA") pursuant to which ArQule
delivered certain of its Mapping Array-TM- compounds to Cubist, and Cubist
screened those compounds against certain of its proprietary targets;

     WHEREAS, Cubist detected activity of certain ArQule compounds against
Cubist certain Cubist targets;

     WHEREAS, pursuant to the terms of the MTA, ArQule and Cubist have
negotiated this Agreement to expand their joint research activities and to
pursue further development of the active compounds discovered by Cubist.

     NOW, THEREFORE, ArQule and Cubist hereby agree as follows:

1.   Definitions.

     1.1. "Active Compound" means any ArQule Compound which exhibits confirmed
significant functional activity against a Target, as determined by the Research
Committee.

     1.2. "Affiliate" means any legal entity (such as a corporation, 
partnership, or limited liability company) that is controlled by a party.  
For the purposes of this definition, the term "control"" means (i) beneficial 
ownership of at least fifty percent (50%) of the voting securities of a 
corporation or other business organization with voting securities or (ii) a 
fifty percent (50%) or greater interest in the net assets or profits of a 
partnership or other business organization without voting securities.

                                       
<PAGE>


     1.3. "ArQule Compound" means a small organic chemical molecule that is
synthesized by ArQule and provided by ArQule to Cubist under this Agreement, as
well as Derivatives of such ArQule Compound.

     1.4. "Array" means a set of ArQule Compounds consisting of diverse,
structurally related small organic chemical compounds arranged in a spatially
addressable format such as a microliter screening plate.

     1.5. "Available Compound" means an ArQule Compound that is not (i) licensed
or otherwise committed to a third party in the Field or (ii) committed to an
internal ArQule program in the Field.  "Available Active Compound" means an
Active Compound that is also an Available Compound.

     1.6. "Chemical Theme" means the chemical or structural characteristics
shared by a group of Active Compounds, as determined by the Research Committee.

     1.7. "Clinical Candidate" means a Collaboration Compound that the Research
Committee has selected for Clinical Development.

     1.8. "Clinical Development" means the clinical development of a compound
after an IND is filed and approved, including Phase I, Phase II and Phase III
Clinical Trials, and resulting in the filing of a complete NDA.

     1.9. "Clinical Development Plan" means a plan for Clinical Development of
one or more Clinical Candidates as approved by the Research Committee and the
Steering Committee for a Collaboration Project.  The Clinical Development Plan
will include a detailed description of the specific responsibilities of each
party for various Clinical Development activities, or plans to oursource certain
tasks, and a proposed timetable for accomplishment of certain objectives for the
Collaboration Project.

     1.10.  "Collaboration" means the collaborative research and development
program described in Article 3 of this Agreement.

     1.11.  "Collaboration Compound" means any Available Active Compound
designated by the Research Committee as a Collaboration Compound pursuant to
Subsection 3.3.(d) or 3.4.(e).

     1.12.  "Collaboration Project" means a project for the Lead
Optimization, Preclinical Development, and Clinical Development of one 


                                       2
<PAGE>

or more Collaboration Compounds for a Target, as approved by the Research
Committee and the Steering Committee.

     1.13.  "Collaborator" means any third party with whom a party enters 
into an agreement pursuant to which such party grants or receives rights in
proprietary technology, intellectual property, or the commercial value of a
product.  For example, an ArQule Collaborator shall include a third party who
participates in a Mapping Array Program or Directed Array Program, and a Cubist
Collaborator shall include a third party who obtains license rights to Cubist
Patent Rights and Cubist Technology.

     1.14.  "Commercialization Plan" means a plan for the commercialization
of a Collaboration Compound as approved by the Steering Committee.

     1.15.  "Confidential Information" means any technical or business
information furnished by one party (the "Disclosing Party") to the other party
(the "Receiving Party") in connection with this Agreement.  Such Confidential
Information may include, without limitation, the identity of a chemical
compound, the use of a chemical compound, trade secrets, know-how, inventions,
technical data or specifications, testing methods, business or financial
information, research and development activities, Steering Committee reports,
Research Committee reports, royalty reports, product and marketing plans, and
customer and supplier information.

     1.16.  "Derivative" means a chemical compound structurally derived in
one or more steps from an ArQule Compound by a process of modification or
partial substitution of at least one component wherein at least one structural
feature is retained at each process step.  The number of intermediate steps or
compounds is not relevant to the classification of a compound as a "Derivative
Compound." A compound need not have any structural similarity to another
compound in order to be classified as a Derivative Compound.

     1.17.  "Directed Array-TM-" means Array of ArQule Compounds based on one
or more Collaboration Compounds that have the same Chemical Theme and that
exhibit activity for the same Target, which Arrays shall be synthesized by
ArQule for Lead Optimization.  The term "Directed Array" is a trademark owned by
ArQule.  The process of synthesizing and testing Directed Arrays based on a
Collaboration Compound is known as a "Directed Array Program."

     1.18.  "FDA" means the United States Food and Drug Administration (or
its foreign equivalent in Japan or Europe).


                                       3
<PAGE>


     1.19.  "Field" means human and animal therapeutic applications, as well
as diagnostic applications intended for use with such therapeutic products.

     1.20.  "IND" means an investigational new drug application filed with
the FDA prior to beginning clinical trials in humans or any comparable
application filed with the regulatory authorities of a country other than the
United States, prior to beginning clinical trials in humans in that country.

     1.21.  "Lead Optimization" means the iterative synthesis and testing of
analogs and derivatives of a compound in connection with a biological target to
identify a compound that exhibits certain optimal characteristics, such as
maximal activity, minimal toxicity, and an acceptable initial bioavailability
and pharmacokinetic, profile.

     1.22.  "Mapping Array-TM-" means an Array of ArQule Compounds that
ArQule generally makes available to its collaborators for screening on a
non-exclusive basis.  The term "Mapping Array" is a trademark owned by ArQule. 
The term "Mapping Array Program" generally describes an arrangement under which
ArQule provides a collaborator with Mapping Arrays and the collaborator screens
the Mapping Arrays on a non-exclusive basis, and specifically describes the
arrangement between ArQule and Cubist as set forth in Section 3.3.

     1.23.  "NDA" means a New Drug Application, as such term is defined by
the FDA, and any equivalent filing in a foreign jurisdiction.

     1.24.  "Patent Rights" means any United States patent application and
any divisional, continuation, or continuation-in-part of such patent application
(to the extent the claims are directed to subject matter specifically described
therein), as well as any patent issued thereon and any reissue or reexamination
of such patent, and any foreign counterparts to such patents and patent
applications.  "ArQule Patent Rights" means Patent Rights that are either (i)
assigned solely to ArQule, (ii) assigned jointly to ArQule and a party other
than Cubist, or (iii) licensed to ArQule, in each case to the extent that ArQule
has the ability to license or sublicense the rights required under this
Agreement.  "Cubist Patent Rights" means Patent Rights that are either (i)
assigned solely to Cubist, (ii) assigned jointly to Cubist and a party other
than ArQule, or (iii) licensed to Cubist, in each case to the extent that Cubist
has the ability to license or sublicense the rights required under this
Agreement.  "Joint Patent Rights" means Patent Rights assigned to both ArQule
and Cubist 


                                      4
<PAGE>

as joint owners.  Joint Patent Rights will include (i) Patent Rights claiming
Joint Technology and (ii) Patent Rights claiming both ArQule Technology and
Cubist Technology in a single filing.

     1.25.  "Phase I Clinical Trials" means clinical trials in a small number
of patients to determine the metabolism and pharmacologic actions of a product
in humans, the side effects associated with increasing doses and to gather
evidence on effectiveness and meeting the requirements established by the FDA
for Phase I clinical trials.

     1.26.  "Phase II Clinical Trials" means clinical trials in a small
sample of the intended patient population to assess the efficacy for a specific
indication of a compound proposed to be used as a therapeutic pharmaceutical
product, to determine dose tolerance and the optimal dose range as well as to
gather additional information relating to safety and potential adverse effects,
and meeting the requirements established by the FDA for Phase II clinical
trials.

     1.27.  "Phase III Clinical Trials" means clinical trials designed to
demonstrate safety and efficacy of a compound proposed to be used as a
therapeutic pharmaceutical product in an expanded patient population at
geographically dispersed study sites, meeting the requirements established by
the FDA for Phase III clinical trials.

     1.28.  "Preclinical Candidate" means a Collaboration Compound that the
Research Committee has selected for Preclinical Development.

     1.29.  "Preclinical Development" means the performance of animal testing
and other preclinical development activities that are required by the FDA to
file a complete IND.

     1.30.   Preclinical Development Plan" means a plan for Preclinical
Development of one or more Preclinical Candidates as approved by the Research
Committee and the Steering Committee for a Collaboration Project.  The
Preclinical Development Plan will include a detailed description of the specific
responsibilities of each party for various Preclinical Development activities
and a proposed timetable for accomplishment of certain objectives for the
Collaboration Project.

     1.31.  "Research Committee" means the Research Committee described in
Section 2. 1.

     1.32.  "Research Materials" means any tangible research materials,
whether biological, chemical, physical, or otherwise, including without

                                          5
<PAGE>
limitation all ArQule Compounds and Cubist assay reagents.  "Proprietary
Research Materials" means any Research Materials that a party designates as
proprietary or confidential, including without limitation all Mapping Array 
compounds and Directed Array compounds.

     1.33.  "Research Plan" means a plan for Lead Optimization of one or more
Collaboration Compounds as approved by the Research Committee and the Steering
Committee for a Collaboration Project.  The Research Plan will include a
detailed description of the specific responsibilities of each party for various
Lead Optimization activities and a proposed timetable for accomplishment of
certain objectives for the Collaboration Project.

     1.34.  "Steering Committee" means the Steering Committee described in
Section 2.2. of this Agreement.

     1.35.  "Sublicensee" means any non-Affiliate third party licensed by a
party to make, have made, use, or sell any Royalty-Bearing Product.

     1.36.  "Target" means each biological or molecular target selected by
Cubist for use in the Collaboration and for which Cubist has certain expertise
or proprietary technology, or both.

     1.37.  "Technology" it means any proprietary development, idea, design,
concept, technique, process, invention, Research Material, discovery, or
improvement, whether or not patentable or copyrightable.  "ArQule Technology"
means Technology that is either (i) assigned solely to ArQule, (H) assigned
jointly to ArQule and a party other than Cubist, or (iii) licensed to ArQule, in
each case to the extent that ArQule has the ability to license or sublicense the
rights required under this Agreement.  "Cubist Technology" means Technology that
is either (i) assigned solely to Cubist, (ii) assigned jointly to Cubist and a
party other than ArQule, or (iii) licensed to Cubist, in each case to the extent
that Cubist has the ability to license or sublicense the rights required under
this Agreement.  "Joint Technology" means Technology that is developed or
discovered jointly by one or more employees or consultants of Cubist and one or
more employees or consultants of ArQule in connection with the Collaboration.

2.   Management of Research Program.

     2.1. Research Committee.

          (a)  Creation of Research Committee.  The parties hereby create a
Research Committee which shall consist of four (4) members.


                                        6
<PAGE>

  Cubist shall designate two (2) members and ArQule shall designate two (2)
members.  If any member of the Research Committee dies, resigns, or becomes
incapacitated, the party which designated such member shall designate his or her
successor (whose term shall commence immediately), and any party may withdraw
the designation of any of its members of the Research Committee and designate a
replacement (whose term shall commence immediately) at any time by giving notice
of the withdrawal and replacement to the other party.  The chairperson of the
Research Committee shall be designated annually on an alternating basis between
the parties.  The initial chairperson shall be designated by the Research
Committee at its first meeting.  The party not designating the chairperson shall
designate one of its representatives as secretary to the Research Committee for
such year.

          (b)  Meetings of the Research Committee.  Regular meetings of the
Research Committee shall be held within forty-five (45) days of the end of each
calendar quarter, or at such other times as the parties may deem appropriate, at
such times and places as the members of the Research Committee shall from time
to time agree.  Special meetings of the Research Committee may be called by
either party on ten (10) days written notice to the other party unless notice is
waived by the parties.  All meetings shall alternate between the offices of the
parties unless the parties otherwise agree.  The chairperson shall be
responsible for sending notice of meetings to all members.  In the event a
Research Committee member is unable to attend a meeting of the Research
Committee, such Research Committee member may designate an alternate member who
will serve solely for that Research Committee meeting.

          (c)  Decisions of Research Committee.  A quorum of the Research
Committee shall be present at any meeting of the Research Committee if at least
one representative of each party is present at such meeting in person or by
telephone.  If a quorum exists at any meeting, the unanimous consent of all
members of the Research Committee present at such meeting is required to take
any action on behalf of the Research Committee.  Unless otherwise specifically
stated to the contrary herein, no individual party shall purport to act on
behalf of the other party unless and then only to the extent authorized to do so
by the Research Committee.

          (d)  Responsibilities of Research Committee.  The Research Committee
shall be responsible for the day-to-day conduct and progress of the
Collaboration, including without limitation:

               (i)   directing and administering the Collaboration;


                                       7
<PAGE>

               (ii)  providing a forum for the exchange of scientific 
                     information among the scientists participating in 
                     the Collaboration;

               (iii) determining the criteria of significant functional
                     activity necessary for an ArQule Compound to qualify 
                     as an Active Compound;

               (iv)  confirming that an ArQule Compound qualifies as an Active
                     Compound and designating such Active Compounds as
                     Collaboration Compounds;

               (v)   reviewing test reports provided by Cubist as to the
                     significant functional activity of each Collaboration
                     Compound in the Mapping Arrays and, based on such results,
                     determining which Collaboration Compounds and Chemical
                     Themes will be used in a Directed Array Program, with the
                     scope of each Chemical Theme determined on the basis of the
                     following criteria: (1) the specific reaction or reaction
                     sequence used to combine members of two or more discrete
                     chemical units in which each chemical unit bears the
                     functional group(s) required for the specific reaction(s)
                     that result in the combination of the chemical units; and
                     (2) the extent to which a class of compounds is related by
                     a recurring structural motif associated with a particular
                     biological activity;

               (vi)  selecting Mapping Arrays for delivery to Cubist under
                     Subsection 3.3. (a);

               (vii) determining the appropriate number of compounds that
                     ArQule should generate in a Directed Array based on
                     Collaboration Compounds with the same Chemical Theme, and
                     determining the appropriate amount of each compound in a
                     Directed Array that ArQule should deliver Cubist for 
                     further research and development with the relevant Target;

              (viii) determining whether to conduct Preclinical Development
                     of any Preclinical Candidate, as

                                        8
<PAGE>


                     well as the scope of such Preclinical Development;

               (ix)  determining and updating the list of Collaboration
                     Compounds, Preclinical Candidates, and Clinical Candidates
                     for each Target;

               (x)   resolving matters involving scientific questions;

               (xi)  preparing and updating the Research Plan, Preclinical
                     Development Plan, and Clinical Development Plan; and

               (xii) monitoring and managing Clinical Development
                     activities.

          (e)  Research Committee Reports.  Within ten (10) days following each
meeting of the Research Committee held pursuant to Subsection 2.1. (b), the
secretary of the Research Committee shall prepare and send to each party a
written report of actions taken at the meeting in such form and containing such
detail as shall be determined by the Research Committee.

          (f)  Deadlock.  In the event that the Research Committee cannot reach
agreement with respect to any matter that is subject to its decision-making
authority, then the matter shall be referred to the Steering Committee for
resolution.

     2.2. Steering Committee.

          (a)  Creation of Steering Committee.  The parties hereby also create a
Steering Committee which shall consist of four (4) members: (i) the Chief
Executive Officer or President of Cubist; (H) the Chief Executive Officer or
President of ArQule; (iii) the Director of Business Development at Cubist (or
such other similar position designated by Cubist from time to time) and (iv) the
Director of Business Development at ArQule (or such other similar position
designated by ArQule from time to time).  If any member of the Steering
Committee dies, resigns, or becomes incapacitated, the party which designated
such member shall designate his or her successor (whose term shall commence
immediately), and any party may withdraw the designation of any of its members
of the Steering Committee and designate a replacement (whose term shall commence
immediately) at any time by giving notice of the withdrawal 


                                       9
<PAGE>


and replacement to the other party.  The chairperson of the Steering Committee
shall be designated annually on an alternating basis between the parties.  The
party not designating the chairperson shall designate one of its representatives
as secretary of the Steering Committee for such year.

          (b)  Meetings of the Steering Committee.  Regular meetings of the
Steering Committee shall be   held within forty-five (45) days of the end of
each calendar year, or at such other times as the parties may deem appropriate,
at such times and places as the members of the Steering Committee shall from
time to time agree.  Special meetings of the Steering Committee may be called by
either party on fifteen (15) days written notice to the other party unless
notice is waived by the parties.  All meetings shall alternate between the
offices of the parties unless the parties otherwise agree.  In the event a
Steering Committee member is unable to attend a meeting of the Steering
Committee, such Steering Committee member may designate an alternate member who
will serve solely for that Steering Committee meeting.

          (c)  Decisions of the Steering Committee.  Unless otherwise
specifically designated as a responsibility of the Research Committee pursuant
to Subsection 2.1. (d), all decisions regarding the contractual and financial
relationship created by this Agreement shall be made by the Steering Committee
acting in accordance with this Agreement or by agents duly authorized in writing
by the Steering Committee.  A quorum of the Steering Committee shall be present
at any meeting of the Steering Committee if the President or Chief Executive
Officer of each party is present at such meeting in person or by telephone.  If
a quorum exists at any meeting, the unanimous consent of all members of the
Steering Committee present at such meeting is required to take any action on
behalf of the Steering Committee.  Unless otherwise specifically stated to the
contrary herein, no individual party shall purport to act on behalf of the other
party unless and then only to the extent authorized to do so by the Steering
Committee.

          (d)  Responsibility of Steering Committee.  The Steering Committee
shall be responsible for approving long-term objectives for, and evaluating the
progress of, the Collaboration and joint Clinical Development activities,
including without limitation:


     (i)   approval of all Research Plans, Preclinical Development Plans,
           Clinical Development Plans and all subsequent decisions regarding the
           direction and priority of all such plans;

                                      10
<PAGE>


     (ii)  reviewing and approving all third party collaborations involving the
           Research Plans, Preclinical Development Plans, and Clinical
           Development Plans;

     (iii) approval of all Clinical Development activities and associated
           expenses for Clinical Candidates; and

     (iv)  developing a Commercialization Plan and managing commercialization of
           Collaboration Compounds.

          (e)  Steering Committee Reports.  Within ten (10) days following each
meeting of the Steering Committee held pursuant to Subsection 2.2.(b), the
secretary of the Steering Committee shall prepare and send to the members of the
Steering Committee a detailed written report of actions taken at the meeting in
such form and containing such detail as shall be determined by the Steering
Committee.

          (f)  Deadlock.  In the event that the Steering Committee cannot reach
agreement within sixty (60) days as to any matter that is subject to its
decision-making authority, then (i) if the matter relates to this Agreement as a
whole, either party may terminate the Agreement in accordance with Section 8.4.
or (ii) if the matter relates only to specific activities under this Agreement,
such as designation of Active Compounds as Collaboration Compounds, the
initiation or conduct of Lead Optimization and Preclinical Development, the
initiation or conduct of Clinical Development, or approval of commercialization
plans, then the deadlock provision in the Agreement that is applicable to that
circumstance shall apply.

3.   Collaboration.

     3.1. Overview of Collaboration.  The overall purposes of this Collaboration
are (i) to screen Mapping Arrays to find ArQule Compounds that demonstrate
significant functional activity against selected Targets, (ii) to designate
certain of these Active Compounds as Collaboration Compounds that are committed
to the program, (iii) to perform Lead Optimization through a Directed Array
Program on certain of these Collaboration Compounds to develop one or more
Preclinical Candidates, (iv) to conduct Preclinical Development of these
Preclinical Candidates, and (v) to conduct Clinical Development of Preclinical
Candidates that successfully complete Preclinical Development and become
Clinical Candidates.  The initial screening will be conducted by Cubist under
the ArQule Mapping Array Program described below.  All Lead Optimization, 


                                       11
<PAGE>

     Preclinical Development, and Clinical Development activities will be
conducted by both parties on a project-by-project basis in accordance with a
Research Plan, Preclinical Development Plan, or Clinical Development Plan
approved by the parties.  Commercial exploitation of a Collaboration Compound
will proceed under a Commercialization Plan.  Separate Collaboration Projects
may be established in the discretion of the Research Committee based on the
relatedness of the Active Compounds and Targets identified.  These Collaboration
Projects may be conducted in series or in parallel at the discretion of the
Research Committee.  A Collaboration Project may terminate due to completion,
withdrawal of a party, deadlock of the parties, or lack of merit.

     3.2. Expenses and Revenues.

          (a)  Expenses Prior to Clinical Development.  [          ]* shall bear
the costs and expenses of its respective activities in connection with this
Collaboration prior to Clinical Development and shall promptly make payments to
third parties arising therefrom.  Neither party shall represent to creditors or
vendors that such party has any authority to obligate or bind the other party,
and shall affirmatively correct any misconception to that effect.  Neither party
shall use the name of the other party in connection with such transactions
without the prior written consent of the other party, which consent may be
withheld in its sole discretion.

          (b)  Expenses of Clinical Development.  [          ]* shall pay
[                   ]* of any direct expenses incurred in connection with
Clinical Development activities approved by the Steering Committee.  Prior to
commencement of any activities for Clinical Development or commercialization of
a Clinical Candidate, the Steering Committee shall establish guidelines and
procedures that will set forth the operational details of this arrangement.  The
Steering Committee may revise these operational guidelines and procedures in its
discretion.

          (c)  Revenues.  [          ]* shall receive [                   ]* of
all proceeds received in connection with commercialization of a Collaboration
Compound arising from the Collaboration.

     3.3. Conduct of Mapping Array Program.

          (a)  Delivery of Mapping Arrays.  Cubist acknowledges prior receipt of
Mapping Arrays #[                                                    


*    Confidential Treatment Requested:  material has been omitted and filed
     separately with the Commission.

                                      12
<PAGE>


   ]* pursuant to a Material Transfer and Screening Agreement dated June 4, 1996
between the parties, which prior agreement is hereby canceled and replaced by
this Agreement. The Research Committee shall select additional Mapping Arrays
for screening by Cubist. ArQule shall promptly deliver the selected Mapping
Arrays to Cubist. The delivered Mapping Arrays will have the standard ArQule
format of one ArQule Compound per well in 96 well microliter plates. Unless
ArQule otherwise notifies the Research Committee, each Mapping Array will
contain approximately the following amounts of each ArQule Compound in that
Array: [                                                                   
                                                                           
                                                                    ]* Cubist 
shall not attempt to identify any compounds in the Mapping Arrays.

          (b)  Identification of Active Compounds.  ArQule hereby grants Cubist
a nonexclusive, worldwide license (without the right to sublicense) under, the
ArQule Patent Rights and other rights in ArQule Technology to screen the
delivered Mapping Array compounds against any Targets in the Field. Cubist
agrees to screen the delivered Mapping Array compounds expeditiously and in a
scientifically sound manner. Cubist shall promptly disclose to ArQule the array
plate number and well number of any Active Compounds. ArQule will promptly
determine whether the Active Compounds are Available Compounds and notify Cubist
of such determination. If an Active Compound is not an Available Compound,
Cubist shall have no rights with respect to that Active Compound.  For Available
Active Compounds, ArQule shall disclose to Cubist the chemical composition and
structure of those Active Compounds, and Cubist shall disclose to ArQule the
identity of the Target, level of activity, and a description of the primary
assays used to detect the activity. All such information disclosed by ArQule
and Cubist shall be deemed Confidential Information and, as such, is subject to
the restrictions set forth in Article 6.

          (c)  Confirmation of Activity.  For a period of [               ]*
after the date upon which ArQule and Cubist exchange information about an Active
Compound pursuant to Section 3.3.(b) (the "Reservation Period"), ArQule will
reserve that Active Compound to the Collaboration. During the Reservation
Period, ArQule will provide Cubist with reasonable additional quantities of that
Active Compound and Cubist will perform secondary screens to confirm the
activity of that Active Compound. The Research Committee will coordinate these
confirmatory screening efforts.

 

*  Confidential Treatment Requested:  material has been omitted and filed
   separately with the Commission.


                                      13
<PAGE>

          (d)  Designation of Collaboration Compounds.  At any time during the
Reservation Period, Cubist may request that the Research Committee designate the
relevant Active Compound as a Collaboration Compound under this Agreement. 
After receiving this request, the Research Committee will confirm that the
compound exhibits the requisite functional activity to qualify as an Active
Compound, whereupon the Research Committee shall designate the relevant Active
Compound as a Collaboration Compound under this Agreement. If the Research
Committee fails to designate an ArQule Compound as a Collaboration Compound,
then (i) Cubist shall have no rights with respect to that ArQule Compound and
(ii) ArQule shall have the right to license or otherwise commit such ArQule
Compound to a third party for any biological target and to include such ArQule
Compound in an ArQule internal discovery program for an unrelated biological
target, subject in both cases to the restrictions on Confidential Information
set forth in Article 6. If the Research Committee does designate an ArQule
Compound as a Collaboration Compound, then ArQule shall (i) internally designate
the Collaboration Compound as committed to Cubist under this Agreement, (ii)
remove the Collaboration Compound from future shipments of its Mapping Arrays,
and (iii) undertake no internal program on the Target for which that
Collaboration Compound exhibits activity.

          (e)  Termination of Mapping Array Program.  The Mapping Array Program
described in this Section 3.3. will commence on the Effective Date and will
continue during the term of this Agreement; provided that either party may
terminate the Mapping Array Program before the expiration or termination of this
Agreement with written notice to the other party which is received at least
sixty (60) days prior to any anniversary of the Effective Date.  In the event of
early termination, Cubist shall immediately cease primary screens of the Mapping
Array compounds but may (i) continue performing confirmatory screens of
previously identified Active Compounds and (ii) request that the Research
Committee designate any Active Compounds as Collaboration Compounds. all in
accordance with the terms of this Agreement.

     3.4. Conduct of Lead Optimization and Preclinical Development Activities.

          (a)  Approval and Initiation of Project.  At any time after an Active
Compound is identified, but no later than sixty (60) days after the relevant
Active Compound becomes a Collaboration Compound, the Research Committee may
approve a proposal for the Lead Optimization and Preclinical Development of one
or more Active Compounds for a Target.  The Research Committee shall forward
such proposals to the Steering Committee for approval. Once the Steering
Committee approves a proposal, the proposed 


                                     14
<PAGE>

research and development project shall automatically be designated a
Collaboration Project under this Agreement.  A Collaboration Project may be
initiated by the parties at any time after the relevant Active Compounds have
been designated as Collaboration Compounds by the Research Committee pursuant to
Subsection 3.3.(d). If the Research Committee or Steering Committee fails to
approve a proposed Lead Optimization or Preclinical Development project for one
or more Collaboration Compounds for a Target because of withdrawal of a party or
deadlock of the Steering Committee, the Collaboration Compound will be subject
to compulsory commercialization pursuant to Subsection 3.4.(h). If the Research
Committee or Steering Committee fails to approve a proposed Lead Optimization or
Preclinical Development project for one or more Collaboration Compounds for a
Target because of lack of business or scientific merit, the reversion provisions
set forth in Subsection 3.4.(i) shall automatically take effect unless otherwise
agreed by the parties.

          (b)  Preparation and Approval of Research Plan and Preclinical
Development Plan.  Promptly following initiation of a Collaboration Project, the
Research Committee shall prepare and submit to the Steering Committee (i) a
proposed Research Plan for Lead Optimization of the relevant Collaboration
Compounds to identify Preclinical Candidates and (ii) a preliminary Preclinical
Development Plan for the Preclinical Development of any Preclinical Candidates
that may be so identified.  Unless otherwise decided by the Research Committee,
the Research Plan shall provide that all Collaboration Compounds will be
submitted to a Directed Array Program for Lead Optimization.  The Steering
Committee must approve the proposed Research Plan and the preliminary
Preclinical Development Plan before the parties commence performance of the
Collaboration Project.  Before the parties commence any Preclinical Development
activities, the Steering Committee must approve a final Preclinical Development
Plan that is prepared and submitted by the Research Committee.  The Research
Committee will also prepare and submit to the Steering Committee any proposed
modifications to previously approved Research Plans and Preclinical Development
Plans.  No such modifications will take effect until approved by the Steering
Committee.

          (c)  Responsibilities for Project.  The parties intend that, in any
Collaboration Project, ArQule will have general responsibility for tasks
involving chemistry and Cubist will have general responsibility for tasks
involving biology.  However, the Research Committee will determine the actual
tasks of each party for each Collaboration Project in accordance with an
approved Research Plan or Preclinical Development Plan.  If the Research
Committee cannot agree upon the allocation of any task for a Collaboration
Project, the matter shall be decided by the Steering Committee.  If the 


                                     15
<PAGE>

Steering Committee cannot resolve the matter within sixty (60) days after the
Research Committee deadlocked, the tasks at issue will be performed by the party
that has general responsibility for that task, as described Exhibit A.

          (d)  Reports and Records.  Each party agrees to promptly and regularly
communicate to the other party all research results from a Collaboration
Project, including quarterly reports to the Research Committee detailing all
tests conducted and results obtained by such party in connection with a
Collaboration Project.  Each party shall prepare and maintain adequate records,
including bound laboratory notebooks maintained in accordance with standard
scientific procedures, containing all appropriate data reflecting all research
results from a Collaboration Project.  In addition, each party shall retain
under appropriate conditions any necessary or desirable samples of Research
Materials that are developed or used in a Collaboration Project.

          (e)  Designation of Additional Collaboration Compounds.  In the course
of a Collaboration Project, Cubist is likely to detect additional Active
Compounds for the relevant Target as it screens Directed Arrays derived from the
Collaboration Compounds.  After the Research Committee confirms that these
ArQule Compounds exhibit the requisite functional activity to qualify as Active
Compounds and ArQule confirms that the Active Compounds are Available Compounds,
the Research Committee will designate such Active Compounds as additional
Collaboration Compounds under this Agreement.

          (f)  Designation of Preclinical Candidates.  The Research Committee
shall monitor Lead Optimization activities in each Collaboration Project.  At
the discretion of the Research Committee, but prior to commencement of any
Preclinical Development activities for a Collaboration Project, the Research
Committee shall designate one or more Collaboration Compounds as Preclinical
Candidates for that Collaboration Project.  Thereafter, the Research Committee
shall have discretion to designate additional Collaboration Compounds as
Preclinical Candidates and to eliminate Collaboration Compounds as Preclinical. 
Candidates for that Collaboration Project as circumstances warrant.  The parties
shall designate a Preclinical Candidate before commencing Preclinical. 
Development activities with a Collaboration Compound in a Collaboration Project.

          (g)  Cross-Licenses for Lead Optimization and Preclinical Development.
The following license grants shall have effect only with respect to activities
undertaken in connection with and during the term of a Collaboration Project and
as approved by the Research Committee:
 
                                      16
<PAGE>


     (i)  ArQule hereby grants Cubist a worldwide, [            ]*, exclusive
          (except as to ArQule) license under the ArQule Patent Rights and other
          rights in ArQule Technology to perform Lead Optimization and
          Preclinical Development in the Field with any Collaboration Compound.

     (ii) Cubist hereby grants ArQule a worldwide, [            ]*, exclusive
          (except as to Cubist) license under the Cubist Patent Rights and other
          rights in Cubist Technology to perform Lead Optimization and
          Preclinical Development in the Field with any Collaboration Compound.

Each party acknowledges and agrees that these cross-licenses, while effective
for a Collaboration Compound, preclude any further license grants in the Field
by either party for that Collaboration Compound.  Neither party shall have the
right to sublicense the license grants set forth in this Section.  During the
term of a Collaboration Project, neither party shall grant any right or license
under the applicable Joint Patent Rights or other rights in Joint Technology to
any third party without the prior written consent of the other party.

          (h)  Withdrawal or Deadlock.  In the event that a party desires to
withdraw from a proposed or ongoing project for Lead Optimization or Preclinical
Development for one or more Collaboration Compounds for a Target, or if the
Steering Committee deadlocks regarding (i) approval of a proposed Lead
Optimization and Preclinical Development project pursuant to Subsection 3.4.(a)
or (ii) an issue that arises in an ongoing Collaboration Project, the parties
will immediately cease work on the Collaboration Project and attempt to
outlicense the work product of that Collaboration Project.  At the request of
either party, the parties will select a mutually acceptable technology broker
who shall have authority to license such work product on their behalf.  If the
parties cannot select a mutually acceptable technology broker within thirty (30)
days, each party will select a third party representative and these
representatives will select the technology broker.  If neither party desires to
use a technology broker, the parties will jointly market such work product and
jointly negotiate and execute any resulting license agreement.  [          ]*
will pay [                   ]* of any costs and expenses (including without
limitation brokers fees, attorneys fees, and travel expenses) incurred in
connection with any outlicensing activities under this Subsection, and
[          ]* will receive [                   ]* of any income resulting from
such license.  As an alternative to forced commercialization of such work 


*  Confidential Treatment Requested:  material has been omitted and filed
   separately with the Commission.


                                       17
<PAGE>

product, either party may make a buy-out offer to the other party at any time,
but the other party may reject any buy-out offer and seek to outlicense the work
product, in its sole discretion.

          (i)  Lack of Merit.  A Collaboration Project shall terminate
immediately in the event of a decision by the Research Committee or Steering
Committee to terminate the Collaboration Project for lack of scientific or
business merit.  In such event, the reversion provisions set forth below shall
automatically take effect unless otherwise agreed by the parties:

     (i)   Cubist shall have no further rights under the ArQule Patent Rights or
           ArQule Technology with respect to such Collaboration Compounds;

     (ii)  ArQule shall have no further rights under the Cubist Patent Rights or
           Cubist Technology with respect to such Collaboration Compounds;

     (iii) Cubist shall grant ArQule an exclusive, worldwide,
           [            ]* license (with the right to sublicense) under any 
           Joint Patent Rights and other rights in Joint Technology to the 
           extent applicable to the composition of such Collaboration Compounds,
           provided that ArQule shall not assert such rights against any Cubist
           Collaborator that discovers such Collaboration Compounds independent
           of any information (whether or not published) derived from either
           party or arising from the Collaboration;

     (iv)  ArQule retains the right to assert all ArQule Patent Rights and other
           rights in ArQule Technology against Cubist and any Cubist
           Collaborator;

     (v)   ArQule shall grant Cubist an exclusive, worldwide, [             ]*
           license (with the right to sublicense) under any Joint Patent Rights
           and other rights in Joint Technology to the extent applicable to the
           use of such Collaboration Compounds with the identified Targets,
           provided that Cubist shall not assert such rights against any ArQule
           Collaborator that discovered such use independent of any information
           (whether or not published) derived from either party or arising from
           the Collaboration; and


*  Confidential Treatment Requested:  material has been omitted and filed
   separately with the Commission.

                                      18
<PAGE>

     (vi)  Cubist retains the right to assert all Cubist Patent Rights and other
           rights in Cubist Technology against ArQule and any ArQule
           Collaborator.

Each party shall remain subject to the restrictions on Confidential Information
set forth in Article 6. Cubist acknowledges that ArQule shall have the right 
to [




               ]*  ArQule acknowledges that Cubist shall have the right (i) to
screen and develop compounds other than those Collaboration Compounds, and (ii)
to screen and develop those Collaboration Compounds if such compounds are
independently discovered by a third party who, on its own initiative, offered
those compounds to Cubist for use with the identified Target.

     3.5. Clinical Development of Collaboration Compounds.

          (a)  Designation of Clinical Candidate.  After approval of an IND for
a Preclinical Candidate, the Research Committee may designate that Preclinical
Candidate as a Clinical Candidate for the purposes of this Section 3.5. Neither
party will commence Clinical Development of any Collaboration Compound or
Derivative before such compound has been designated as a Clinical Candidate in
accordance with this Section.  The Steering Committee will develop a
Commercialization Plan for each Clinical Candidate.

          (b)  Co-Development Right.  Without further action, each party shall
have the co-exclusive right to conduct the Clinical Development, commercial
license, manufacture, distribution, marketing, and sale of any Clinical
Candidate.

          (c)  Authority.  The parties shall have joint responsibility for and
control over all activities for the Clinical Development and commercialization
of the relevant Clinical Candidate, in accordance with the Clinical Development
Plan and Commercialization Plan.  The Steering Committee shall decide whether to
proceed with each stage of Clinical Development and shall have oversight,
management, and approval authority for commercialization decisions, activities,
and agreements.  The Research Committee shall have oversight and management
authority for Clinical Development activities.  Unless otherwise agreed by the
parties, any grant of commercial rights 


*  Confidential Treatment Requested:  material has been omitted and filed
   separately with the Commission.

                                      19
<PAGE>

in a Clinical Candidate shall require the signatures of both parties to become
effective.

          (d)  Development Licenses.  The following license grants shall have
effect only with respect to activities approved by the Steering Committee and
undertaken in connection with the Clinical Development of the relevant Clinical
Candidate:

     (i)  ArQule hereby grants Cubist a worldwide, [               ]*, exclusive
          (except as to ArQule) license under the ArQule Patent Rights, Joint
          Patent Rights, and other rights in ArQule Technology and Joint
          Technology to perform Clinical Development of the Clinical Candidate.

     (ii) Cubist hereby grants ArQule a worldwide, [               ]*, exclusive
          (except as to Cubist) license under the Cubist Patent Rights, Joint
          Patent Rights, and other rights in Cubist Technology and Joint
          Technology to perform Clinical Development of the Clinical Candidate.

Each party acknowledges and agrees that these cross-licenses, while effective
for Clinical Candidate, preclude any further license grants in the Field by
either party for the Clinical Development of that Clinical Candidate.  Neither
party shall have the right to sublicense the license grants set forth in this
Subsection without the approval of the Research Committee or Steering Committee,
as appropriate.

          (e)  Withdrawal and Deadlock.  Each party shall have the right to
decline to participate in, or to withdraw from, Clinical Development activities
for a particular Clinical Candidate at any time upon sixty (60) days prior
written notice to the other party.  In such event, the relevant Collaboration
Project shall terminate upon the conclusion of the sixty-day notice period.  In
the event that the Steering Committee reaches deadlock on an issue that arises
in connection with Clinical Development or commercialization activities for a
particular Clinical Candidate, the Collaboration Project shall immediately
terminate.  If a Collaboration Project terminates due to withdrawal or deadlock
under this Section, the parties will immediately cease work on the Collaboration
Project and attempt to outlicense the work product of that Collaboration
Project.  At the request of either party, the parties will select a mutually
acceptable technology broker who shall have authority to license such work
product on their behalf.  If the parties cannot select a mutually acceptable
technology broker within thirty 


*    Confidential Treatment Requested:  material has been omitted and filed
     separately with the Commission.

                                      20
<PAGE>

(30) days, each party will select a third party representative and these
representatives will select the technology broker.  If neither party desires to
use a technology broker, the parties will jointly market such work product and
jointly negotiate and execute any resulting license agreement.  [          ]*
will pay [                   ]* of any direct costs and expenses (including
without limitation brokers fees, attorneys fees, and travel expenses) incurred
in connection with any outlicensing activities under this Subsection, and
[          ]* will receive [                   ]* of all proceeds resulting from
such license.  As an alternative to forced commercialization of such work
product, either party may make a buy-out offer to the other party at any time,
but the other party may reject any buy-out offer and seek to outlicense the work
product, in its sole discretion.

          (f)  Lack of Merit.  In the event of a decision by the Research
Committee or Steering Committee to terminate Clinical Development or
commercialization activities for a Clinical Candidate for lack of clinical or
business merit, the development licenses set forth in Subsection 3.5.(d) shall
automatically and immediately terminate and the reversion provisions set forth
below shall automatically take effect unless otherwise agreed by the parties:

     (i)  Cubist shall have no further rights under the ArQule Patent Rights or
          ArQule Technology with respect to such Clinical Candidate and all
          other Collaboration Compounds within that Collaboration Project;

     (ii) ArQule shall have no further rights under the Cubist Patent Rights or
          Cubist Technology with respect to such Clinical Candidate and all
          other Collaboration Compounds within that Collaboration Project;

    (iii) Cubist shall grant ArQule an exclusive, worldwide, [               ]*
          license (with the right to sublicense) under any Joint Patent Rights 
          and other rights in Joint Technology to the extent applicable to the 
          composition of such Clinical Candidate and all other Collaboration 
          Compounds within that Collaboration Project, provided that ArQule 
          shall not assert such rights against any Cubist Collaborator that 
          discovers such Collaboration Compounds independent of any information
          (whether or not published) derived from either party or arising from 
          the Collaboration;


*  Confidential Treatment Requested:  material has been omitted and filed
   separately with the Commission.


                                      21
<PAGE>

     (iv) ArQule retains the right to assert all ArQule Patent Rights and other
          rights in ArQule Technology against Cubist and any Cubist
          Collaborator;

     (v)  ArQule shall grant Cubist an exclusive, worldwide, [               ]*
          license (with the right to sublicense) under any Joint Patent Rights
          and other rights in Joint Technology to the extent applicable to the
          use of such Clinical Candidate and all other Collaboration Compounds
          within that Collaboration Project with the identified Targets,
          provided that Cubist shall not assert such rights against any ArQule
          Collaborator that discovered such use independent of any information
          (whether or not published) derived from either party or arising from
          the Collaboration; and

     (vi) Cubist retains the right to assert all Cubist Patent Rights and other
          rights in Cubist Technology against ArQule and any ArQule
          Collaborator.

Each party shall remain subject to the restrictions on Confidential Information
set forth in Article 6. Cubist acknowledges that ArQule shall have the right [




                                        ]*  ArQule acknowledges that Cubist
shall have the right (i) to screen and develop compounds other than the
Collaboration Compounds within the terminated Collaboration Project, and (ii) to
screen and develop those Collaboration Compounds if such compounds are
independently discovered by a third party who, on its own initiative, offered
those compounds to Cubist for use with the identified Target.

4.   Ownership and Management of Intellectual Property.

    4.1.  Intellectual Property Developed Outside of Collaboration.  Except as
expressly set forth in this Agreement, neither party shall have any rights in
Patent Rights and Technology that is developed or discovered by the other party
prior to the Effective Date or outside of the Collaboration.  For example,
Cubist shall have sole ownership of all right, title, and interest in Targets
and other Cubist Proprietary Research Materials, and ArQule shall 


*    Confidential Treatment Requested:  material has been omitted and filed
     separately with the Commission.

                                     22
<PAGE>

have sole ownership of all right, title, and interest in ArQule Compounds
provided to Cubist in the Mapping Array Program.  Each party shall have sole
responsibility for and control over Patent Rights claiming any of its Technology
that was developed or discovered prior to the Effective Date or outside of the
Collaboration.  Neither party shall have any right to review and comment on such
Patent Rights of the other party.

    4.2.  Ownership of Intellectual Property Arising From the Collaboration. 
Ownership of Patent Rights and Technology arising from the Collaboration shall
be allocated in the following manner:

     [
      

     
     

     
                                   ]*

Each party shall ensure that its employees, consultants, agents, and
representatives are contractually required to assign to such party all Patent
Rights and other rights in Technology arising from the Collaboration and to
promptly disclose to such party all patentable inventions within that
Technology.

     4.3. Notice of Intellectual property Arising From the Collaboration.  Each
party shall provide prompt written notice to the Research Committee of the
internal disclosure of any significant Technology developed by its personnel in
connection with the Collaboration.

     4.4. Responsibility for Patent Rights Arising from the Collaboration. 
ArQule shall be responsible for and shall control, [        ]*, the preparation,
filing, prosecution, grant, and maintenance of any Patent Rights claiming only
ArQule Technology and shall consult with Cubist on, and give Cubist a reasonable
opportunity to review, all such filings to the extent they directly relate to
the Collaboration.  Cubist shall be responsible for and shall control,
[        ]* the preparation, filing, prosecution, grant, and maintenance of all
Patent Rights claiming only Cubist Technology and shall consult with ArQule on,
and give ArQule a reasonable opportunity to review, 


*  Confidential Treatment Requested:  material has been omitted and filed
   separately with the Commission.

                                     23

<PAGE>

all such filings to the extent they relate directly to the Collaboration.  In
the case of Joint Technology, the Research Committee will decide whether to seek
Joint Patent Rights claiming that Technology or to maintain that Technology as a
trade secret.  The Research Committee will also decide whether to seek Patent
Rights claiming both ArQule Technology and Cubist Technology in one filing,
which also constitutes a Joint Patent Right.  If the Research Committee decides
to seek any Joint Patent Rights, the parties shall jointly prepare, file,
prosecute, and maintain such Patent Rights, and all related expenses shall
become equally by the parties.  Notwithstanding the foregoing, neither party
shall file any Joint Patent Rights claiming the composition or use of any Active
Compound in a Mapping Array until the Research Committee has properly designated
that Active Compound as a Collaboration Compound in accordance with Subsection
3.3.(d) or 3.4.(e).

     4.5. Assumption of Rights by Other Party.  In the event that a party
desires to decline responsibility for obtaining or maintaining Patent Rights in
a country for any of its Technology that is developed or discovered in
connection with the Collaboration, such party will notify the other party before
taking such action and, upon request, will allow the other party to assume
responsibility for, and all expenses relating to, the relevant Patent Rights in
those countries; provided, however, that neither party shall have the right to
seek patent protection for any Technology that a party has decided, in its
discretion, to maintain as a trade secret.  In the event that a party desires to
cease further payment of patent-related expenses for a Joint Patent Right in any
country, such party may assign to the other party all rights in that Joint
Patent Right in such country and thereafter have no further obligation to pay
such expenses.

     4.6. Cooperation.  Each party agrees to cooperate fully in the preparation,
filing, prosecution, and maintenance of all Patent Rights claiming Technology
arising from the Collaboration.  Such cooperation includes, without limitation,
(i) promptly executing all papers and instruments, or requiring its employees,
consultants, and agents to execute such papers and instruments, as reasonable
and appropriate so as to enable one or both parties to file, prosecute, and
maintain such Patent Rights in any country; (ii) promptly informing the other
party of matters that may affect the preparation, filing, prosecution, or
maintenance of any such Patent Rights; and (iii) undertaking no actions that are
potentially deleterious to the preparation, filing, or prosecution of any such
Patent Rights.

     4.7. Abandonment of Joint Patent Rights.  In the event that the parties
fail to complete a Collaboration Project due to lack of merit pursuant to
Subsection 3.4.(i), the parties shall discuss in good faith 

                                      24
<PAGE>


whether to abandon any unpublished patent applications within the Joint Patent
Rights relating to that Collaboration Project.  The parties recognize that
publication of such Joint Patent Rights could adversely affect each of their
interests after reversion occurs under Subsection 3.4.(i).

5.   Research Materials.

     5.1. Ownership of Research Materials.  In the course of this Collaboration,
one party (the "Provider") may transfer to the other party (the "Recipient")
certain of its Research Materials.  The Recipient acknowledges and agrees that
such Research Materials are and shall be owned by the Provider.  The Recipient
agrees to execute and deliver any documents of assignment or conveyance to
effectuate the ownership rights of the Provider in such Research Materials.  [
     
     
     
     
          ]*

     5.2. Use and Transfer of Research Materials.  Except as otherwise agreed by
the Research Committee, the Recipient agrees to use Research Materials provided
by the Provider solely for purposes set forth in this Agreement and shall not
distribute such Research Materials to any third party other than its employees
and consultants who are working on the Collaboration.

     5.3. Additional Restrictions for Property Research Materials.  In the case
of Proprietary Research Materials furnished by a Provider, Recipient agrees (i)
not to transfer such Proprietary Research Materials to any third party without
the prior written consent of the Provider, (ii) to permit access to the
Proprietary Research Materials only to its employees and consultants requiring
such access, (iii) to inform such employees and consultants of the proprietary
nature of the Proprietary Research Materials, and (iv) to take reasonable
precautions, at least as stringent as those observed by Recipient to protect its
own proprietary materials, to ensure that such employees and consultants observe
the obligations of Recipient under this Section.

     5.4. Disposition of Unused Research Materials.  At the request of Provider,
Recipient will return or destroy any unused Research Materials furnished by
Provider.


*  Confidential Treatment Requested:  material has been omitted and filed
   separately with the Commission.


                                      25
<PAGE>


     5.5. Compliance with Law.  Recipient agrees to comply with all federal,
state, and local laws and regulations applicable to the use, storage, disposal,
and transfer of Research Materials furnished by Provider, including without
limitation the Toxic Substances Control Act (15 USC 2601 et seq.) and
implementing regulations (in particular, 40 CFR 720.36 [Research and Development
Exemption]), the Food, Drug, and Cosmetic Act (21 USC 301 g et seq.) and
implementing regulations, and all Export Administration Regulations of the
Department of Commerce.  Recipient assumes sole responsibility for any violation
of such laws or regulations by Recipient or any of its Affiliates or
Sublicensees.

     5.6. Limitation of Liability.  Any Research Materials delivered pursuant to
this Agreement are understood to be experimental in nature and may have
hazardous properties. Recipient should assume that the compounds are dangerous
and should use appropriate precautions.  [





                                             .]*

6.   Confidential Information.

     6.1. Designation of Confidential Information.  Confidential Information
that is disclosed in writing shall be marked with a legend indicating its
confidential status.  Confidential Information that is disclosed orally or
visually shall be documented in a written notice prepared by the Disclosing
Party and delivered to the Receiving Party within thirty (30) days of the date
of disclosure; such notice shall summarize the Confidential Information
disclosed to the Receiving Party and reference the time and place of disclosure.

     6.2. Obligations of Receiving Party.  The Receiving Party agrees that it
     shall:

     (i)  maintain all Confidential Information in strict confidence, except
          that the Receiving Party may disclose or permit the disclosure of any
          Confidential Information to its directors, officers, employees,
          consultants, and advisors who are obligated to maintain the
          confidential nature of such Confidential 


*  Confidential Treatment Requested:  material has been omitted and filed
   separately with the Commission.

                                      26
<PAGE>


          Information and who need to know such Confidential Information for the
          purposes set forth in this Agreement;

     (ii) use all Confidential Information solely for the purposes of this
          Agreement; and

    (iii) allow its directors, officers, employees, consultants, and advisors to
          reproduce the Confidential Information only to the extent necessary 
          to effect the purposes set forth in this Agreement, with all such
          reproductions being considered Confidential Information,

     6.3. Exceptions.  The obligations of the Receiving Party under Section 6.2.
above shall not apply to the extent that the Receiving Party can demonstrate
that certain Confidential Information:

     (i)  was in the public domain prior to the time of its disclosure under
          this Agreement;

     (ii) entered the public domain after the time of its disclosure under this
          Agreement through means other than an unauthorized disclosure
          resulting from an act or omission by the Receiving Party;

    (iii) was independently developed or discovered by the Receiving Party
          without use of the Confidential Information;

     (iv) is or was disclosed to the Receiving Party at any time, whether prior
          to or after the time of its disclosure under this Agreement, by a
          third party having no fiduciary relationship with the Disclosing Party
          and having no obligation of confidentiality to the Disclosing Party
          with respect to such Confidential Information; or

     (v)  is required to be disclosed to comply with applicable laws or
          regulations (such as disclosure to the FDA or the United States Patent
          and Trademark Office or to their foreign equivalents), or to comply
          with a court or administrative order, provided that the Disclosing
          Party receives prior written notice of such disclosure and that the
          Receiving Party takes all reasonable and lawful actions to obtain
          confidential treatment for such disclosure and, if possible, to
          minimize the extent of such disclosure.


                                      27
<PAGE>



     6.4. Return of Confidential Information.  Upon the termination of this
Agreement, or earlier at the request of the Disclosing Party, the Receiving
Party shall return to the Disclosing Party all originals, copies, and summaries
of documents, materials, and other tangible manifestations of Confidential
Information in the possession or control of the Receiving Party, except that the
Receiving Party may retain one copy of the Confidential Information in the
possession of its legal counsel solely for the purpose of monitoring its
obligations under this Agreement.

     6.5. Survival of Obligations.  The obligations set forth in this Article
shall remain in effect for an item of Confidential Information for a period of
ten (10) years after the date upon which a Receiving Party first received that
Confidential Information, except that the obligation of the Receiving Party to
return Confidential Information to the Disclosing Party shall survive until
fulfilled.

7.   Indemnification and Insurance.

     7.1. General Indemnification.  [          ]* (the "Indemnifying Party")
shall indemnify and hold harmless the other party, its Affiliates, and their
respective directors, officers, employees and agents (collectively, the
"Indemnitees ") from and against all claims, expenses or liability of whatever
nature arising from any default, act, omission or negligence of the Indemnifying
Party, its agents or employees, or others exercising rights by, through, or
under the Indemnifying Party, or the failure of the Indemnifying Party or such
persons to comply with any applicable laws, rules, regulations, codes,
ordinances or directives of governmental authorities, in each case to the extent
the same are related, directly or indirectly, to the Collaboration described
herein; provided, however, that in no event shall the Indemnifying Party be
obligated under this section to indemnify the Indemnitees where such claim,
expense or liability results solely from any omission, fault, negligence, or
other misconduct of any of the Indemnitees.

     7.2. Procedure.  The Indemnitees agree to provide the Indemnifying Party
with prompt written notice of any claim, suit, action, demand, or judgment for
which indemnification is sought under this Agreement.  If an Indemnitee fails to
provide such notice within a reasonable time, and if such failure prejudicially
affects the ability of the Indemnifying Party to defend such action, the
Indemnifying Party shall be relieved of its liability to such Indemnitee under
this Article 7. The Indemnifying Party agrees, at its own expense, to provide
attorneys reasonably acceptable to the Indemnitees to 


*  Confidential Treatment Requested:  material has been omitted and filed
   separately with the Commission.

                                      28
<PAGE>

defend against any such claim.  The Indemnitees shall cooperate fully with the
Indemnifying Party in such defense and will permit the Indemnifying Party to
conduct and control such defense and the disposition of such claim, suit, or
action (including all decisions relative to litigation, appeal, and settlement);
provided, however, that any Indenmitee shall have the right to retain its own
counsel, at the expense of the Indemnifying Party, if representation of such
Indemnitee by the counsel retained by the Indemnifying Party would be
inappropriate because of actual or potential differences in the interests of
such Indemnitee and any other party represented by such counsel.  The
Indemnifying Party agrees to keep the other party informed of the progress in
the defense and disposition of such claim and to consult with such party with
regard to any proposed settlement.

8.   Term and Termination.

     8.1. Term.  This Agreement shall commence on the Effective Date and shall
continue for a period of ten (10) years unless earlier terminated pursuant to
this Article 8.

     8.2. Voluntary Termination.  At any time on or after the first anniversary
of the Effective Date, either party may terminate this Agreement immediately
upon [                                       ]* notice to the other party.

     8.3. Termination for Default.  In the event that either party commits a
material breach of its obligations under this Agreement and fails to cure that
breach within [            ]* days after receiving written notice thereof, the
other party may terminate this Agreement [                        ]* notice to 
the party in breach.

     8.4. Termination for Deadlock.  In the event of a deadlock in the Steering
Committee on a matter that affects the Agreement as a whole, as described in
Subsection 2.2.(f), either party may terminate this Agreement
[                          ]* notice to the other party.

     8.5. Force Majeure.  Neither party will be responsible for delays resulting
from acts beyond the control of such party, provided that the nonperforming
party uses commercially reasonable efforts to avoid or remove such causes of
nonperformance and continues performance hereunder with reasonable dispatch
whenever such causes are removed.


*  Confidential Treatment Requested:  material has been omitted and filed
   separately with the Commission.


                                      29
<PAGE>


     8.6. Effect of Termination.  Except as otherwise agreed by the parties,
upon the expiration or termination of this Agreement, the provisions of
Subsections 3.3.(e), 3.4.(h), and 3.5.(c) shall immediately apply to all ongoing
activities of the Collaboration and the other provisions of this Agreement shall
immediately terminate, except that the following provisions shall survive:
Articles 4, 5, 6, 7, and 9; Sections 8.6., 10.1, 10.7., and 10.9.

9.   Dispute Resolution.

     9.1. Procedures Mandatory.  The parties agree that any dispute arising out
of or relating to this Agreement shall be resolved solely by means of the
procedures set forth in this Article, and that such procedures constitute
legally binding obligations that are an essential provision of this Agreement;
provided, however, that all procedures and deadlines specified in this Article
may be modified by written agreement of the parties.  If either party fails to
observe the procedures of this Article, as modified by their written agreement,
the other party may bring an action for specific performance in any court of
competent jurisdiction.

     9.2. Dispute Resolution Procedures.

          (a)  Negotiation.  In the event of any dispute arising out of or
relating to this Agreement, the affected party shall notify the other party, and
the parties shall attempt in good faith to resolve the matter within ten (10)
days after the date such notice is received by the other party (the "Notice
Date").  Any disputes not resolved by good faith discussions shall be referred
to the Steering Committee, which shall meet at a mutually acceptable time and
location within thirty (30) days after the Notice Date and attempt to negotiate
a settlement.

     (b)  Mediation.  If the matter remains unresolved within sixty (60) days
after the Notice Date, or if the Steering Committee fails to meet within thirty
(30) days after the Notice Date, either party may initiate mediation upon
written notice to the other party, whereupon both parties shall be obligated to
engage in a mediation proceeding under the then current Center for Public
Resources ("CPR") Model Procedure for Mediation of Business Disputes, except
that specific provisions of this Section shall override inconsistent provisions
of the CPR Model Procedure. The mediator will be selected from the CPR Panels
of Neutrals. If the parties cannot agree upon the selection of a mediator
within ninety (90) days after the Notice Date, then upon the request of either
party, the CPR shall appoint the mediator. The parties shall attempt to resolve
the dispute through mediation until one of the following occurs: (i) the parties
reach a written settlement; (ii) the mediator notifies the parties in writing
that they have reached an impasse; 

                                      30
<PAGE>

(iii) the parties agree in writing that they have reached an impasse; or (iv)
the parties have not reached a settlement within one hundred and twenty (120)
days after the Notice Date.

          (c)  [                .]*  If the parties fail to resolve the dispute
through mediation, or if neither party elects to initiate mediation, each party
shall have the right to pursue any other remedies legally available to resolve
the dispute, [
                         .]*

     9.3. Preservation of Rights Pending Resolution.

          (a)  Performance to Continue.  Each party shall continue to perform
its obligations under this Agreement pending final resolution of any dispute
arising out or relating to this Agreement; provided, however, that a party may
suspend performance of its obligations during any period in which the other
party fails or refuses to perform its obligations.

          (b)  Provisional Remedies.  [
          
                                   ]* either party may seek a preliminary
injunction or other provisional equitable relief if, in its reasonable judgment,
such action is necessary to avoid irreparable harm to itself or to preserve its
rights under this Agreement.

          (c)  Statute of Limitations.  The parties agree that all applicable
statutes of limitation and time-based defenses (such as estoppel and laches)
shall be tolled while the procedures set forth in Subsections 9.2.(a) and 9.2(b)
are pending.  The parties shall take any actions necessary to effectuate this
result.

10.  Miscellaneous.

     10.1.  Publicity.  No press release, advertising, promotional sales
literature, or other promotional oral or written statements to the public in
connection with or alluding to work performed under this Agreement or the
relationship between the parties created by it, having or containing any
reference to ArQule or Cubist, shall be made by either party without the prior
written approval of the other party, except for restatements of
previously-approved statements and disclosures required by applicable law or
regulation.

*  Confidential Treatment Requested:  material has been omitted and filed
   separately with the Commission.

                                      31
<PAGE>

     10.2.  Relationship of Parties.  For the purposes of this Agreement,
each party is an independent contractor and not an agent or employee of the
other party.  Neither party shall have authority to make any statements,
representations, or commitments of any kind, or to take any action which shall
be binding on the other party, except as may be explicitly provided for herein
or authorized in writing.

     10.3.  Counterparts.  This Agreement may be executed in one or more
counterparts, each of which shall be deemed an original, and all of which
together shall be deemed to be one and the same instrument.

     10.4.  Headings.  All headings in this Agreement are for convenience
only and shall not affect the meaning of any provision hereof,

     10.5.  Binding Effect.  This Agreement shall inure to the benefit of and
be binding upon the parties and their respective lawful successors and assigns.

     10.6.  Assignment.  This Agreement may not be assigned by either party
without the prior written consent of the other party, except that either of the
parties may assign this Agreement to a successor in connection with the merger,
consolidation, or sale of all or substantially all of its assets or that portion
of its business pertaining to the subject matter of this Agreement.

     10.7.  Notices.  All notices, requests, demands and other communications
required or permitted to be given pursuant to this Agreement shall be in writing
and shall be deemed to have been duly given upon the date of receipt if
delivered by hand, recognized national overnight courier, confirmed facsimile
transmission, or registered or certified mail, return receipt requested, postage
prepaid, to the following addresses or facsimile numbers:

If to Cubist:

                    Cubist Pharmaceuticals, Inc.
                    24 Emily Street
                    Cambridge, MA 02139
                    Attn:  Scott M. Rocklage, President
                    Tel:  (617) 576-1999
                    Fax:  (617) 576-0232


                                      32
<PAGE>

If to ArQule:

                    ArQule, Inc.
                    200 Boston Avenue
                    Medford, MA 02155
                    Attn:  Eric B. Gordon, President
                    Tel:  (617) 395-4100
                    Fax:  (617) 395-1225

with a copy (which shall not constitute notice) to:

                    Palmer & Dodge
                    One Beacon Street
                    Boston, MA 02108
                    Attn:  Michael Lytton, Esq.
                    Tel:  (617) 573-0327
                    Fax:  (617) 227-4420

Either party may change its designated address and facsimile number by notice to
the other party in the manner provided in this Section.

     10.8.  Amendment and Waiver.  This Agreement may be amended,
supplemented, or otherwise modified at any time, but only by means of a written
instrument signed by both parties.  Any waiver of any rights or failure to act
in a specific instance shall relate only to such instance and shall not be
construed as an agreement to waive any rights or fail to act in any other
instance, whether or not similar.

     10.9.  Governing Law.  This Agreement and the legal relations among the
parties shall be governed by and construed in accordance with the laws of the
Commonwealth of Massachusetts irrespective of any conflict of laws principles.

     10.10. Severability.  In the event that any provision of this Agreement
shall, for any reason, be held to be invalid or unenforceable in any respect,
such invalidity or unenforceability shall not affect any other provision hereof,
and this Agreement shall be construed as if such invalid or unenforceable
provision had not been included herein.

     10.11. Entire Agreement.  This Agreement constitutes the entire agreement
between the parties with respect to the subject matter hereof and supersedes any
and all prior or contemporaneous oral and prior written agreements and
understandings including, without limitation, a certain 


                                     33
<PAGE>

Material Transfer and Screening Agreement dated June 4, 1996 between the
parties.

     IN WITNESS WHEREOF, the undersigned have duly executed and delivered this
Agreement as a sealed instrument effective as of the date first above written.

                    CUBIST PHARMACEUTICALS, INC.
                    
                    
                    
                    By:  /s/ Mark Carthy
                       -----------------------------------------------
                         Mark Carthy
                         Vice President and Chief Business Officer
                    
                    ARQULE, INC.
                    
                    By:  /s/ Eric B. Gordon
                       -----------------------------------------------
                         Eric B. Gordon,
                         President and Chief Executive Officer



                                      34


<PAGE>

                                                                   Exhibit 10.22
                                          
                            AMENDMENT TO PROMISSORY NOTE



     This Amendment to Promissory Note (this "Amendment") is entered into as of
this 23th day of December, 1997 by and between Cubist Pharmaceuticals, Inc., a
Delaware Corporation, (the "Payee") and Scott M. Rocklage (the "Maker").

     This Amendment is attached to and made part of that certain Secured
Promissory Note, dated as of July 21, 1994 (the "Promissory Note"), in the
principal amount of One Hundred Thirty-One Thousand Six Hundred Eighty-Five
Dollars ($131,685.00) made payable by the Maker to the Payee.

     WHEREAS, the Maker and the Payee wish to amend the Promissory Note.

     NOW, THEREFORE, for the sum of ten and 00/100 Dollars ($10.00) and other
good and valuable consideration the receipt and sufficiency of which are hereby
acknowledged, Maker and Payee hereby amend the Promissory Note as follows:

     The wording "on July 21, 1996 (the "Maturity Date"), and to pay interest on
the principal amount outstanding from time to time hereunder, from the date
hereof through and including the date on which such principal amount is paid in
full, at a rate of four percent (4%) per annum simple interest." appearing in
the fifth line of the first paragraph immediately prior to the words "Interest
hereunder" which was amended to "July 21, 1997" on "Amendment To Promissory
Note" on July 21, 1996 is hereby deleted and replaced with "in equal quarterly
installments of Ten Thousand Dollars ($10,000) payable on the last day of the
quarter commencing on March 31, 1998 and completing on September 30, 2001 with
no further interest due and payable from this date."

     EXCEPT AS SPECIFICALLY AMENDED BY THIS AMENDMENT THE PROMISSORY NOTE
REMAINS UNMODIFIED AND IN FULL FORCE AND EFFECT ACCORDING TO ITS TERMS.

<PAGE>

     IN WITNESS WHEREOF, the undersigned have executed this Amendment as a
sealed instrument as of the date first above written.

                                                   MAKER:




WITNESS:                                            /s/ Scott M. Rocklage 
         ------------------------                   -----------------------
                                                    Scott M. Rocklage


                                                    PAYEE:

                                                    Cubist Pharmaceuticals, Inc.



WITNESS:                                            /s/ John K. Clarke
         ------------------------                   -----------------------
                                                    John K. Clarke
                                                    Chairman of the Board

                                       2

<PAGE>


                                                                   Exhibit 10.33
                            CUBIST PHARMACEUTICALS, INC.
                                  24 Emily Street
                                Cambridge, MA  02139

                                  January 9, 1998
Mr. Mark P. Carthy
21 Stone Road
Belmont, Massachusetts  02178

Dear Mark:

     Reference is hereby made to that certain Letter Agreement, dated as of May
19, 1997 (the "Agreement"), between you and Cubist Pharmaceuticals, Inc., a
Delaware corporation (the "Company"), pursuant to which you exercised your stock
option to purchase 10,000 shares (the "Shares") of the Company's common stock,
$.001 par value per share, at an exercise price of $8.00 per share, and you paid
for the Shares by delivering to the Company a Secured Promissory Note in the
principal amount of $80,000 (the "Note"), which the Company agreed to forgive
over time.  Capitalized terms which are not defined herein shall have the same
meanings as ascribed to such terms in the Agreement.

     You and the Company hereby agree that in the event your employment with the
Company terminates prior to April 11, 2000 and the market value of the Shares on
the date of such termination (the "Termination Date") is less than the principal
and accrued but unpaid interest under the Note at the Termination Date, then,
notwitstanding anything in the Pledge Agreement to the contrary, the Shares
shall be the Company's sole recourse for payment of the Note.  In such event,
you agree to surrender your certificate for the Shares accompanied by a stock
power executed in blank to the Company, and upon such surrender and delivery of
the Shares to the Company, you shall have no further obligation to the Company
with respect to the Note and the Note shall be returned to you marked "Paid In
Full."

     This letter agreement shall be governed by the internal substantive laws of
the Commonwealth of Massachusetts and shall be binding upon the heirs, personal
representatives, executors, administrators, successors and permitted assigns of
the parties.  The rights and obligations of either party under this letter
agreement may only be assigned with the prior written consent of the other party
hereto.  This letter agreement supersedes all prior written and oral agreements
and understandings between the parties and represents the entire agreement
between the parties with respect to the subject matter hereof and may only be
modified or amended pursuant to a written instrument signed by both parties. 
The Company is not by reason of this letter agreement obligated to continue your
employment.



<PAGE>

Mr. Mark P. Carthy
January 9, 1998
Page 2


     If the foregoing accurately reflects our understanding, please so
acknowledge by countersigning this letter agreement in the space provided for
your signature below.

                                        Very truly yours,

                                        CUBIST PHARMACEUTICALS, INC.



                                        By:  /s/ Scott M. Rocklage         
                                             ---------------------------------
                                             Scott M. Rocklage, Ph.D.
                                             President and CEO

Agreed and Accepted
as of this 9th  day of 
December, 1997:



  /s/ Mark Carthy
- ------------------------
Mark P. Carthy
21 Stone Road
Belmont, MA  02178
     

<PAGE>

                                                                   Exhibit 10.34
                                          
                               MASTER LEASE AGREEMENT

Lessor:   TRANSAMERICA BUSINESS CREDIT CORPORATION 
          Riverway II
          West Office Tower
          9399 West Higgins Road
          Rosemont, Illinois 60018

Lessee:   CUBIST PHARMACEUTICALS, INC. 24 Emily Street
              Cambridge, Massachusetts 02139

     The lessor pursuant to this Master Lease Agreement ("Agreement") dated 
as of February 7, 1997, is Transamerica Business Credit Corporation 
("Lessor"). All equipment, together with all present and future additions, 
parts, accessories, attachments, substitutions, repairs, improvements and 
replacements thereof or thereto, which are the subject of a Lease (as defined 
in the next sentence) shall be referred to as "Equipment." Simultaneous with 
the execution and delivery of this Agreement, the parties are entering into 
one or more Lease Schedules (each, a "Schedule") which refer to and 
incorporate by reference this Agreement, each of which constitutes a lease 
(each, a "Lease") for the Equipment specified therein.  Additional details 
pertaining to each Lease are specified in the applicable Schedule.  Each 
Schedule that the parties hereafter enter into shall constitute a Lease.  
Lessor has no obligation to enter into any additional leases with, or extend 
any future financing to, Lessee.

     1.   LEASE. (a) Subject to and upon all of the terms and conditions of 
this Agreement and each Schedule, Lessor hereby agrees to lease to Lessee and 
Lessee hereby agrees to lease from Lessor the Equipment for the Term (as 
defined in Paragraph 2 below) thereof (b) Except as provided below, before 
purchasing any Equipment from a manufacturer or supplier and leasing the same 
to Lessee, Lessor shall have received before the acceptance of the Equipment 
by Lessee an Assignment Agreement in form and substance satisfactory to 
Lessor, executed by Lessee and acknowledged by such manufacturer or supplier 
assigning to Lessor all of Lessee's right, title and interest in and to such 
Equipment and the purchase agreement relating thereto (the "Assignment").  
Upon delivery of such Equipment, Lessee shall transmit to Lessor a properly 
executed Certificate of Acceptance in the form attached hereto covering each 
item of Equipment set forth in such Assignment.  Upon execution by Lessee and 
delivery to Lessor of a Certificate of Acceptance, (x) each item of Equipment 
set forth therein shall be deemed to have been delivered to and irrevocably 
accepted by Lessee for lease hereunder, (y) Lessee shall make payments of 
interim rent ("Interim Rent") at the per them rate set forth in the 
Certificate of Acceptance, and (z) such Certificate of Acceptance shall be 
deemed a Schedule for all purposes hereof, until such time as a Schedule 
covering the Equipment described in the Certificate of Acceptance is executed 
and delivered by Lessee to Lessor.  Interim Rent shall be due on the date 
stated in the Certificate of Acceptance.  On or before the 28th day of the 
last month each calendar quarter, Lessee shall deliver to Lessor a Schedule, 
duly executed by Lessee, covering all Equipment delivered to Lessee through 
the second week of the last month of such calendar quarter for which no 
Schedule was previously delivered.

     2.   TERM.  Each Lease shall be effective and the term of each Lease 
("Term") shall commence on the commencement date specified in the applicable 
Schedule as the same may be adjusted, in the sole discretion of Lessor 
pursuant to an Adjustment Letter (the "Adjustment Letter")(but in no event 
shall any Lease have a commencement date of later than December 31, 1997) 
and, unless sooner terminated (as hereinafter provided), shall expire at the 
end of the term specified in such Schedule; provided, however, that 
obligations due to be performed by Lessee during the Term shall continue 
until they have been performed in full.  Schedules will only be executed 
quarterly..

     3.   RENT.  Lessee shall pay as rent to Lessor, for use of the Equipment 
during the Term or Renewal Term (as defined in Paragraph 8), rental payments 
equal to the sum of all rental payments including, without limitation, 
security deposits, advance rents and interim rents payable in the amounts and 
on the dates specified in the applicable Schedule ("Rent").  If any Rent or 
other amount payable by Lessee is not paid 

<PAGE>

within five days after the day on which it becomes payable, Lessee will pay 
on demand, as a late charge, an amount equal to 5% of such unpaid Rent or 
other amount but only to the extent permitted by applicable law.  All 
payments provided for herein shall be payable to Lessor at its address 
specified above, or at any other place designated by Lessor.

     4.   LEASE NOT CANCELABLE; LESSEE'S OBLIGATIONS ABSOLUTE.  No Lease may 
be canceled or terminated except as expressly provided herein.  Lessee's 
obligation to pay all Rent due or to become due hereunder shall be absolute 
and unconditional and shall not be subject to any delay, reduction, set-off, 
defense, counterclaim or recoupment for any reason whatsoever, including any 
failure of the Equipment or any representations by the manufacturer or the 
vendor thereof.  If the Equipment is unsatisfactory for any reason, Lessee 
shall make any claim solely against the manufacturer or the vendor thereof 
and shall, nevertheless, pay Lessor all Rent payable hereunder.

     5.   SELECTION AND USE OF EQUIPMENT.  Lessee agrees that it shall be 
responsible for the selection, use of, and results obtained from, the 
Equipment and any other associated equipment or services.

     6.   WARRANTIES.  LESSOR MAKES NO REPRESENTATION OR WARRANTY, EXPRESS OR 
IMPLIED, AS TO ANY MATTER WHATSOEVER, INCLUDING, WITHOUT LIMITATION, THE 
DESIGN OR CONDITION OF THE EQUIPMENT OR ITS MERCHANTABILITY, SUITABILITY, 
QUALITY OR FITNESS FOR A PARTICULAR PURPOSE, AND HEREBY DISCLAIMS ANY SUCH 
WARRANTY. LESSEE SPECIFICALLY WAIVES ALL RIGHTS TO MAKE A CLAIM AGAINST 
LESSOR FOR BREACH OF ANY WARRANTY WHATSOEVER.  LESSEE LEASES THE EQUIPMENT 
"AS IS." IN NO EVENT SHALL LESSOR HAVE ANY LIABILITY FOR, NOR SHALL LESSEE 
HAVE ANY REMEDY AGAINST LESSOR FOR, ANY LIABILITY, CLAIM, LOSS, DAMAGE OR 
EXPENSE CAUSED DIRECTLY OR INDIRECTLY BY THE EQUIPMENT OR ANY DEFICIENCY OR 
DEFECT THEREOF OR THE OPERATION, MAINTENANCE OR REPAIR THEREOF OR ANY 
CONSEQUENTIAL DAMAGES AS THAT TERM IS USED IN SECTION 2-719(3) OF THE MODEL 
UNIFORM COMMERCIAL CODE, AS AMENDED FROM TIME TO TIME ("UCC").  Lessor grants 
to Lessee, for the sole purpose of prosecuting a claim, the benefits of any 
and all warranties made available by the manufacturer or the vendor of the 
Equipment to the extent assignable.

     7.   DELIVERY.  Lessor hereby appoints Lessee as Lessor's agent for the 
sole and limited purpose of accepting delivery of the Equipment from each 
vendor thereof.  Lessee shall pay any and all delivery and installation 
charges. Lessor shall not be liable to Lessee for any delay in, or failure 
of, delivery of the Equipment.

     8.   RENEWAL.  So long as no Event of Default or event which, with the 
giving of notice, the passage of time, or both, would constitute an Event of 
Default, shall have occurred and be continuing, or the Lessee shall not have 
exercised its purchase option under Paragraph 9 hereof, each Lease will 
automatically renew for a term of twelve months (the "Renewal Term") on the 
terms and conditions of this Agreement or as set forth in the applicable 
Schedule; provided, however, that Obligations due to be performed by the 
Lessee during the Renewal Term shall continue until they have been performed 
in full. The monthly rental payments for the Renewal Term shall be equal to 
1.25% of the equipment cost plus any monthly sales or use tax.

     9.   PURCHASE OPTION.  So long as no Event of Default or event which, 
with the giving of notice, the passage of time, or both, would constitute an 
Event of Default, shall have occurred and be continuing, Lessee may, upon 
written notice to Lessor received at least one hundred eighty days before the 
expiration of a Term, purchase all, but not less than all, the Equipment 
covered by the applicable Lease on the date specified therefor in the 
applicable Schedule ("Purchase Date").  The purchase price for such Equipment 
shall be its fair market value as set forth in the Schedule on an "In-place, 
In-use" basis, as mutually agreed by Lessor and Lessee, or, if they cannot 
agree, as determined by an independent appraiser selected by Lessor and 
approved by Lessee, which approval will not be unreasonably delayed or 
withheld.  Lessee shall pay the cost of any such appraisal.  So long as no 
Event of Default or event which, with the giving of notice, the passage of 
time, or both, would constitute an Event of Default, shall have occurred and 
be continuing, Lessee may, upon written notice to Lessor received at least 
one hundred eighty days prior to the expiration of the Renewal Term, 

                                      2
<PAGE>

purchase all, but not less than all, the Equipment covered by the applicable 
Schedule by the last date of the Renewal Term (the "Alternative Purchase 
Date") at a purchase price equal to its then fair market value on an 
"In-place, In-use" basis.  On the Purchase Date or the Alternative Purchase 
Date, as the case may be, for any Equipment, Lessee shall pay to Lessor the 
purchase price, together with all sales and other taxes applicable to the 
transfer of the Equipment and any other amount payable and arising hereunder, 
in immediately available funds, whereupon Lessor shall transfer to Lessee, 
without recourse or warranty of any kind, express or implied, all of Lessor's 
right, title and interest in and to such Equipment on an "As Is, Where Is" 
basis.

     10.  OWNERSHIP; INSPECTION; MARKING; FINANCING STATEMENTS.  Lessee shall 
affix to the Equipment any labels supplied by Lessor indicating ownership of 
such Equipment.  The Equipment is and shall be the sole property of Lessor. 
Lessee shall have no right, title or interest therein, except as lessee under 
a Lease.  The Equipment is and shall at all times be and remain personal 
property and shall not become a fixture.  Lessee shall obtain and record such 
instruments and take such steps as may be necessary to prevent any person 
from acquiring any rights in the Equipment by reason of the Equipment being 
claimed or deemed to be real property.  Upon request by Lessor, Lessee shall 
obtain and deliver to Lessor valid and effective waivers, in recordable form, 
by the owners, landlords and mortgagees of the real property upon which the 
Equipment is located or certificates of Lessee that it is the owner of such 
real property or that such real property is neither leased nor mortgaged.  
Lessee shall make the Equipment and its maintenance records available for 
inspection by Lessor at reasonable times and upon reasonable notice.  Lessee 
shall execute and deliver to Lessor for filing any UCC financing statements 
or similar documents Lessor may reasonably request.

     11.  EQUIPMENT USE.  Lessee agrees that the Equipment will be operated 
by competent, qualified personnel in connection with Lessee's business for 
the purpose for which the Equipment was designed and in accordance with 
applicable operating instructions, laws and government regulations, and that 
Lessee shall use all reasonable precautions to prevent loss or damage to the 
Equipment from fire and other hazards.  Lessee shall procure and maintain in 
effect all orders, licenses, certificates, permits, approvals and consents 
required by federal, state or local laws or by any governmental body, agency 
or authority in connection with the delivery, installation, use and operation 
of the Equipment.

     12.  MAINTENANCE.  Lessee, at its sole cost and expense, shall keep the 
Equipment in a suitable environment as specified by the manufacturer's 
guidelines or the equivalent and meet all recertification requirements, and 
shall maintain the Equipment in its original condition and working order, 
ordinary wear and tear excepted.  At the reasonable request of Lessor, Lessee 
shall furnish all proof of maintenance.

     13.  ALTERATION; MODIFICATIONS; PARTS.  Lessee may alter or modify the 
Equipment only with the prior written consent of Lessor.  Any alteration 
shall be removed and the Equipment restored to its normal, unaltered 
condition at Lessee's expense (without damaging the Equipment's originally 
intended function or its value) prior to its return to Lessor.  Any part 
installed in connection with warranty or maintenance service or which cannot 
be removed in accordance with the preceding sentence shall be the property of 
Lessor.

     14.  RETURN OF EQUIPMENT.  Except for Equipment that has suffered a 
Casualty Loss (as defined in Paragraph 15 below) and is not required to be 
repaired pursuant to Paragraph 15 below or Equipment purchased by Lessee 
pursuant to Paragraph 9 above, upon the expiration of the Renewal Term of a 
Lease, or upon demand by Lessor pursuant to Paragraph 22 below, Lessee shall 
contact Lessor for shipping instructions and, at Lessee's own risk, 
immediately return the Equipment, freight prepaid, to a location in the 
continental United States specified by Lessor.  At the time of such return to 
Lessor, the Equipment shall (i) be in the operating order, repair and 
condition as required by or specified in the original specifications and 
warranties of each manufacturer and vendor thereof, ordinary wear and tear 
excepted, and meet all recertification requirements and (ii) be capable of 
being promptly assembled and operated by a third party purchaser or third 
party lessee without further repair, replacement, alterations or 
improvements, and in accordance and compliance with any and all statutes, 
laws, ordinances, rules and regulations of any governmental authority or any 
political subdivision thereof applicable to the use and operation of the 
Equipment.  Except as otherwise provided under Paragraph 9 hereof, at least 
one hundred eighty days before 

                                      3
<PAGE>

the expiration of the Renewal Term, Lessee shall give Lessor notice of its 
intent to return the Equipment at the end of such Renewal Term.  During the 
one hundred eighty-day period prior to the end of a Term or the Renewal Term, 
Lessor and its prospective purchasers or lessees shall have, upon not less 
than two business days' prior notice to Lessee and during normal business 
hours, or at any time and without prior notice upon the occurrence and 
continuance of an Event of Default, the right of access to the premises on 
which the Equipment is located to inspect the Equipment, and Lessee shall 
cooperate in all other respects with Lessor's remarketing of the Equipment.  
The provisions of this Paragraph 14 are of the essence of the Lease, and upon 
application to any court of equity having jurisdiction in the premises, 
Lessor shall be entitled to a decree against Lessee requiring specific 
performance of the covenants of Lessee set forth in this Paragraph 14.  If 
Lessee fails to return the Equipment when required, the terms and conditions 
of the Lease shall continue to be applicable and Lessee shall continue to pay 
Rent until the Equipment is received by Lessor.

     15.  CASUALTY INSURANCE; LOSS OR DAMAGE.  Lessee will maintain, at its 
own expense, liability and property damage insurance relating to the 
Equipment, insuring against such risks as are customarily insured against on 
the type of equipment leased hereunder by businesses in which Lessee is 
engaged in such amounts, in such form, and with insurers satisfactory to 
Lessor; provided, however, that the amount of insurance against damage or 
loss shall not be less than the greater of (a) the replacement value of the 
Equipment and (b) the stipulated loss value of the Equipment specified in the 
applicable Schedule ("Stipulated Loss Value").  Each liability insurance 
policy shall provide coverage (including, without limitation, personal injury 
coverage) of not less than $1,000,000 for each occurrence, and shall name 
Lessor as an additional insured; and each property damage policy shall name 
Lessor as sole loss payee and all policies shall contain a clause requiring 
the insurer to give Lessor at least thirty days prior written notice of any 
alteration in the terms or cancellation of the policy.  Lessee shall furnish 
a copy of each insurance policy (with endorsements) or other evidence 
satisfactory to Lessor that the required insurance coverage is in effect; 
provided, however Lessor shall have no duty to ascertain the existence of or 
to examine the insurance policies to advise Lessee if the insurance coverage 
does not comply with the requirements of this Paragraph.  If Lessee fails to 
insure the Equipment as required, Lessor shall have the right but not the 
obligation to obtain such insurance, and the cost of the insurance shall be 
for the account of Lessee due as part of the next due Rent.  Lessee consents 
to Lessor's release, upon its failure to obtain appropriate insurance 
coverage, of any and all information necessary to obtain insurance with 
respect to the Equipment or Lessor's interest therein.

     Until the Equipment is returned to and received by Lessor as provided in 
Paragraph 14 above, Lessee shall bear the entire risk of theft or destruction 
of, or damage to, the Equipment including, without limitation, any 
condemnation, seizure or requisition of title or use ("Casualty Loss").  No 
Casualty Loss shall relieve Lessee from its obligations to pay Rent except as 
provided in clause (b) below.  When any Casualty Loss occurs, Lessee shall 
immediately notify Lessor and, at the option of Lessor, shall promptly (a) 
place such Equipment in good repair and working order; or (b) pay Lessor an 
amount equal to the Stipulated Loss Value of such Equipment and all other 
amounts (excluding Rent) payable by Lessee hereunder, together with a late 
charge on such amounts at a rate per annum equal to the rate imputed in the 
Rent payments hereunder (as reasonably determined by Lessor) from the date of 
the Casualty Loss through the date of payment of such amounts, whereupon 
Lessor shall transfer to Lessee, without recourse or warranty (express or 
implied), all of Lessor's interest, if any, in and to such Equipment on an 
"AS IS, WHERE IS" basis.  The proceeds of any insurance payable with respect 
to the Equipment shall be applied, at the option of Lessor, either towards 
(i) repair of the Equipment or (ii) payment of any of Lessee's obligations 
hereunder.  Lessee hereby appoints Lessor as Lessee's attorney-in-fact to 
make claim for, receive payment of, and execute and endorse all documents, 
checks or drafts issued with respect to any Casualty Loss under any insurance 
policy relating to the Equipment.

     16.  TAXES.  Lessee shall pay when due, and indemnify and hold Lessor 
harmless from, all sales, use, excise and other taxes, charges, and fees 
(including, without limitation, income, franchise, business and occupation, 
gross receipts, licensing, registration, titling, personal property, stamp 
and interest equalization taxes, levies, imposts, duties, charges or 
withholdings of any nature), and any fines, penalties or interest thereon, 
imposed or levied by any governmental body, agency or tax authority upon or 
in connection with the Equipment, its purchase, ownership, delivery, leasing, 
possession, use or relocation of the Equipment or otherwise in connection 
with the transactions contemplated by each Lease or the Rent thereunder, 
excluding 

                                      4
<PAGE>

taxes on or measured by the net income of Lessor.  Upon request, Lessee will 
provide proof of payment.  Unless Lessor elects otherwise, Lessor will pay 
all property taxes on the Equipment for which Lessee shall reimburse Lessor 
promptly upon request.  Lessee shall timely prepare and file all reports and 
returns which are required to be made with respect to any obligation of 
Lessee under this Paragraph 16.  Lessee shall, to the extent permitted by 
law, cause all billings of such fees, taxes, levies, imposts, duties, 
withholdings and governmental charges to be made to Lessor in care of Lessee. 
 Upon request, Lessee will provide Lessor with copies of all such billings.

     17.  LESSOR'S PAYMENT.  If Lessee fails to perform its obligations under 
Paragraph 15 or 16 above, or Paragraph 23 below, Lessor shall have the right 
to substitute performance, in which case, Lessee shall immediately reimburse 
Lessor therefor.

     18.  GENERAL INDEMNITY.  Each Lease is a net lease.  Therefore, Lessee 
shall indemnify Lessor and its successors and assigns against, and hold 
Lessor and its successors and assigns harmless from, any and all claims, 
actions, damages, obligations, liabilities and all costs and expenses, 
including, without limitation, legal fees, incurred by Lessor or its 
successors and assigns arising out of each Lease including, without 
limitation, the purchase, ownership, delivery, lease, possession, 
maintenance, condition, use or return of the Equipment, or arising by 
operation of law, except that Lessee shall not be liable for any claims, 
actions, damages, obligations and costs and expenses determined by a 
non-appealable, final order of a court of competent jurisdiction to have 
occurred as a result of the gross negligence or willful misconduct of Lessor 
or its successors and assigns.  Lessee agrees that upon written notice by 
Lessor of the assertion of any claim, action, damage, obligation, liability 
or lien, Lessee shall assume full responsibility for the defense thereof, 
provided that Lessor's failure to give such notice shall not limit or 
otherwise affect its rights hereunder.  Any payment pursuant to this 
Paragraph (except for any payment of Rent) shall be of such amount as shall 
be necessary so that, after payment of any taxes required to be paid thereon 
by Lessor, including taxes on or measured by the net income of Lessor, the 
balance will equal the amount due hereunder.  The provisions of this 
Paragraph with regard to matters arising during a Lease shall survive the 
expiration or termination of such Lease.

     19.  ASSIGNMENT BY LESSEE.  Lessee shall not, without the prior written 
consent of Lessor, (a) assign, transfer, pledge or otherwise dispose of any 
Lease or Equipment, or any interest therein; (b) sublease or lend any 
Equipment or permit it to be used by anyone other than Lessee and its 
employees; or (c) move any Equipment from the location specified for it in 
the applicable Schedule, except that Lessee may move Equipment to another 
location within the United States provided that Lessee has delivered to 
Lessor (A) prior written notice thereof and (B) duly executed financing 
statements and other agreements and instruments (all in form and substance 
satisfactory to Lessor) necessary or, in the opinion of the Lessor, desirable 
to protect Lessor's interest in such Equipment.  Notwithstanding anything to 
the contrary in the immediately preceding sentence, Lessee may keep any 
Equipment consisting of motor vehicles or rolling stock at any location in 
the United States.

     20.  ASSIGNMENT BY LESSOR.  Lessor may assign its interest or grant a 
security interest in any Lease and the Equipment individually or together, in 
whole or in part.  If Lessee is given written notice of any such assignment, 
it shall immediately make all payments of Rent and other amounts hereunder 
directly to such assignee.  Each such assignee shall have all of the rights 
of Lessor under each Lease assigned to it.  Lessee shall not assert against 
any such assignee any set-off, defense or counterclaim that Lessee may have 
against Lessor or any other person.

     21.  DEFAULT; NO WAIVER.  Lessee or any guarantor of any or all of the 
obligations of Lessee hereunder (together with Lessee, the "Lease Parties") 
shall be in default under each Lease upon the occurrence of any of the 
following events (each, an "Event of Default"): (a) Lessee fails to pay 
within five days of when due any amount required to be paid by Lessee under 
or in connection with any Lease; (b) any of the Lease Parties fails to 
perform any other provision under or in connection with a Lease or violates 
any of the covenants or agreements of such Lease Party under or in connection 
with a Lease; (c) any representation made or financial information delivered 
or furnished by any of the Lease Parties under or in connection with a Lease 
shall prove to have been inaccurate in any material respect when made; (d) 
any of the Lease Parties makes an 

                                      5
<PAGE>

assignment for the benefit of creditors, whether voluntary or involuntary, or 
consents to the appointment of a trustee or receiver, or if either shall be 
appointed for any of the Lease Parties or for a substantial part of its 
property without its consent and, in the case of any such involuntary 
proceeding, such proceeding remains undismissed or unstayed for forty-five 
days following the commencement thereof-, (e) any petition or proceeding is 
filed by or against any of the Lease Parties under any Federal or State 
bankruptcy or insolvency code or similar law and, in the case of any such 
involuntary petition or proceeding, such petition or proceeding remains 
undismissed or unstayed for forty-five days following the filing or 
commencement thereof, or any of the Lease Parties takes any action 
authorizing any such petition or proceeding; (f) any of the Lease Parties 
fails to pay when due any indebtedness for borrowed money or under 
conditional sales or installment sales contracts or similar agreements, 
leases or obligations evidenced by bonds, debentures, notes or other similar 
agreements or instruments to any creditor (including Lessor under any other 
agreement) after any and all applicable cure periods therefor shall have 
elapsed; (g) any judgment shall be rendered against any of the Lease Parties 
which shall remain unpaid or unstayed for a period of sixty days; (h) any of 
the Lease Parties shall dissolve, liquidate, wind up or cease its business, 
sell or otherwise dispose of all or substantially ail of its assets or make 
any material change in its lines of business; (i) any of the Lease Parties 
shall amend or modify its name, unless such Lease Party delivers to Lessor 
thirty days prior to any such proposed amendment or modification written 
notice of such amendment or modification and within ten days before such 
amendment or modification delivers executed financing statements (in form and 
substance satisfactory to the Lessor); 0) any of the Lease Parties shall 
merge or consolidate with any other entity or make any material change in its 
capital structure, in each case without Lessor's prior written consent, which 
shall not be unreasonably withheld; (k) any of the Lease Parties shall suffer 
any loss or suspension of any material license, permit or other right or 
asset necessary to the profitable conduct of its business, fail generally to 
pay its debts as they mature, or call a meeting for purposes of compromising 
its debts; (1) any of the Lease Parties shall deny or disaffirm its 
obligations hereunder or under any of the documents delivered in connection 
herewith; or (m) there is a change in more than 35% of the ownership of any 
equity interests of any of the Lease Parties on the date hereof or more than 
35% of such interests become subject to any contractual, judicial or 
statutory lien, charge, security interest or encumbrance.

     22.  REMEDIES.  Upon the occurrence and continuation of an Event of 
Default, Lessor shall have the right, in its sole discretion, to exercise any 
one or more of the following remedies: (a) terminate each Lease; (b) declare 
any and all Rent and other amounts then due and any and all Rent and other 
amounts to become due under each Lease (collectively, the "Lease 
Obligations") immediately due and payable; (c) take possession of any or all 
items of Equipment, wherever located, without demand, notice, court order or 
other process of law, and without liability for entry to Lessee's premises, 
for damage to Lessee's property or otherwise; (d) demand that Lessee 
immediately return any or all Equipment to Lessor in accordance with 
Paragraph 14 above, and, for each day that Lessee shall fail to return any 
item of Equipment, Lessor may demand an amount equal to the Rent payable for 
such Equipment in accordance with Paragraph 14 above; (e) lease, sell or 
otherwise dispose of the Equipment in a commercially reasonable manner, with 
or without notice and on public or private bid; (f) recover the following 
amounts from the Lessee (as damages, including reimbursement of costs and 
expenses, liquidated for all purposes and not as a penalty): (i) all costs 
and expenses of Lessor reimbursable to it hereunder,. including, without 
limitation, expenses of disposition of the Equipment, legal fees and all 
other amounts specified in Paragraph 23 below; (ii) an amount equal to the 
sum of (A) any accrued and unpaid Rent through the later of (1) the date of 
the applicable default or (2) the date that Lessor has obtained possession of 
the Equipment or such other date as Lessee has made an effective tender of 
possession of the Equipment to Lessor (the "Default Date") and (B) if Lessor 
resells or re-lets the Equipment, Rent at the periodic rate provided for in 
each Lease for the additional period that it takes Lessor to resell or re-let 
all of the Equipment; (iii) the present value of all future Rent reserved in 
the Leases and contracted to be paid over the unexpired Term of the Leases 
discounted at five percent simple interest per annum; (iv) the reversionary 
value of the Equipment as of the expiration of the Term of the applicable 
Lease as set forth on the applicable Schedule; and (v) any indebtedness for 
Lessee's indemnity under Paragraph 18 above, plus a late charge at the rate 
specified in Paragraph 3 above, less the amount received by Lessor, if any, 
upon sale or re-let of the Equipment; and (g) exercise any other right or 
remedy to recover damages or enforce the terms of the Leases.  Upon the 
occurrence and continuance of an Event of Default or an event which with the 
giving of notice or the passage of time, or both, would result in an Event of 
Default, Lessor shall have the right, whether or not Lessor has made any 
demand or the obligations of Lessee hereunder have matured, to 

                                      6
<PAGE>

appropriate and apply to the payment of the obligations of Lessee hereunder 
all security deposits and other deposits (general or special, time or demand, 
provisional or final) now or hereafter held by and other indebtedness or 
property now or hereafter owing by Lessor to Lessee.  Lessor may pursue any 
other rights or remedies available at law or in equity, including, without 
limitation, rights or remedies seeking damages, specific performance and 
injunctive relief.  Any failure of Lessor to require strict performance by 
Lessee, or any waiver by Lessor of any provision hereunder or under any 
Schedule, shall not be construed as a consent or waiver of any other breach 
of the same or of any other provision.  Any amendment or waiver of any 
provision hereof or under any Schedule or consent to any departure by Lessee 
herefrom or therefrom shall be in writing and signed by Lessor.      

     No right or remedy is exclusive of any other provided herein or 
permitted by law or equity.  All such rights and remedies shall be cumulative 
and may be enforced concurrently or individually from time to time.

     23.  LESSOR'S EXPENSE.  Lessee shall pay Lessor on demand all its 
reasonable expenses which shall not exceed $5,000 without the written consent 
of Lessee (including legal fees and expenses) incurred in connection with the 
preparation, execution and delivery of this Agreement and any other agreement 
and transaction contemplated hereby and all costs and expenses in protecting 
and enforcing Lessor's rights and interests in each Lease and the Equipment, 
including, without limitation, legal, collection and remarketing fees and 
expenses incurred by Lessor in enforcing the terms, conditions or provisions 
of each Lease or, upon the occurrence and continuation of an Event of Default.

     24.  LESSEE'S WAIVERS.  To the extent permitted by applicable law, 
Lessee hereby waives any and all rights and remedies conferred upon a lessee 
by Sections 2A-508 through 2A-522 of the UCC.  To the extent permitted by 
applicable law, Lessee also hereby waives any rights now or hereafter 
conferred by statute or otherwise which may require Lessor to sell, lease or 
otherwise use any Equipment in mitigation of Lessor's damages as set forth in 
Paragraph 22 above or which may otherwise limit or modify any of Lessor's 
rights or remedies under Paragraph 22.  Any action by Lessee against Lessor 
for any default by Lessor under any Lease shall be commenced within one year 
after any such cause of action accrues.

     25.  NOTICES; ADMINISTRATION.  Except as otherwise provided herein, all 
notices, approvals, consents, correspondence or other communications required 
or desired to be given hereunder shall be given in writing and shall be 
delivered by overnight courier, hand delivery or certified or registered 
mail, postage prepaid, if to Lessor, then to Technology Finance Division, 76 
Batterson Park Road, Farmington, Connecticut 06032, Attention: Assistant Vice 
President, Lease Administration, with a copy to Lessor at Riverway 11, West 
Office Tower, 9399 West Higgins Road, Rosemont, Illinois 60018, Attention: 
Legal Department, if to Lessee, then to Cubist Pharmaceuticals, Inc., 24 
Emily Street, Cambridge, Massachusetts 02139, Attention: Director: Finance 
and Administration or such other address as shall be designated by Lessee or 
Lessor to the other party. All such notices and correspondence shall be 
effective when received.

     26.  REPRESENTATIONS.  Lessee represents and warrants to Lessor that (a) 
Lessee is duly organized, validly existing and in good standing under the 
laws of the State of its incorporation; (b) the execution, delivery and 
performance by Lessee of this Agreement are within Lessee's powers, have been 
duly authorized by all necessary action, and do not contravene (i) Lessee's 
organizational documents or (ii) any law or contractual restriction binding 
on or affecting Lessee; (c) no authorization or approval or other action by, 
and no notice to or filing with, any governmental authority or regulatory 
body is required for the due execution, delivery and performance by Lessee of 
this Agreement; (d) each Lease constitutes the legal, valid and binding 
obligations of Lessee enforceable against Lessee in accordance with its 
terms; (e) the cost of each item of Equipment does not exceed the fair and 
usual price for such type of equipment purchased in like quantity and 
reflects all discounts, rebates, and allowances for the Equipment (including, 
without limitation, discounts for advertising, prompt payment, testing or 
other services) given to the Lessee by the manufacturer, supplier or any 
other person; and (f) all information supplied by Lessee to Lessor in 
connection herewith is correct and does not omit any material statement 
necessary to insure that the information supplied is not misleading.

                                      7
<PAGE>


     27.  FURTHER ASSURANCES.  Lessee, upon the request of Lessor, will 
execute, acknowledge, record or file, as the case may be, such further 
documents and do such further acts as may be reasonably necessary, desirable 
or proper to carry out more effectively the purposes of this Agreement.  
Lessee hereby appoints Lessor as its attorney-in-fact to execute on behalf of 
Lessee and authorizes Lessor to file without Lessee's signature any UCC 
financing statements and amendments Lessor deems advisable.

     28.  FINANCIAL STATEMENTS.  Lessee shall deliver to Lessor: (a) as soon 
as available, but not later than 120 days after the end of each fiscal year 
of Lessee and its consolidated subsidiaries, the consolidated balance sheet, 
income statement and statements of cash flows and shareholders equity for 
Lessee and its consolidated subsidiaries (the "Financial Statements") for 
such year, reported on by independent certified public accountants without an 
adverse qualification; and (b) as soon as available, but not later than 60 
days after the end of each of the first three fiscal quarters in any fiscal 
year of Lessee and its consolidated subsidiaries, the Financial Statements 
for such fiscal quarter, together with a certification duly executed by a 
responsible officer of Lessee that such Financial Statements have been 
prepared in accordance with generally accepted accounting principles and are 
fairly stated in all material respects (subject to normal year-end audit 
adjustments).  Lessee shall also deliver to Lessor as soon as available 
copies of all press releases and other similar communications made by Lessee.

     29.  CONSENT TO JURISDICTION.  Lessee irrevocably submits to the 
jurisdiction of any Illinois state or federal court sitting in Illinois for 
any action or proceeding arising out of or relating to this Agreement or the 
transactions contemplated hereby, and Lessee irrevocably agrees that all 
claims in respect of any such action or proceeding may be heard and 
determined in such Illinois state or federal court.

     30.  WAIVER OF JURY TRIAL.  LESSEE AND LESSOR IRREVOCABLY WAIVE ALL 
RIGHT TO TRIAL BY JURY IN ANY ACTION, PROCEEDING OR COUNTERCLAIM ARISING OUT 
OF OR RELATING TO THIS AGREEMENT OR THE TRANSACTIONS CONTEMPLATED HEREBY.

     31.  FINANCE LEASE.  Lessee and Lessor agree that each Lease is a 
"Finance Lease" as defined by Section 2A-103(g) of the UCC.  Lessee 
acknowledges that Lessee has reviewed and approved each written Supply 
Contract (as defined by UCC 2A-103(y)) covering Equipment purchased from each 
"Supplier" (as defined by UCC 2A- 103 (x)) thereof

     32.  NO AGENCY.  Lessee acknowledges and agrees that neither the 
manufacturer or supplier, nor any salesman, representative or other agent of 
the manufacturer or supplier, is an agent of Lessor.  No salesman, 
representative or agent of the manufacturer or supplier is authorized to 
waive or alter any term or condition of this Agreement or any Schedule and no 
representation as to the Equipment or any other matter by the manufacturer or 
supplier shall in any way affect Lessee's duty to pay Rent and perform its 
other obligations as set forth in this Agreement or any Schedule.

     33.  SPECIAL TAX INDEMNIFICATION.  Lessee acknowledges that Lessor, in 
determining the Rent due hereunder, has assumed that certain tax benefits as 
are provided to an owner of property under the Internal Revenue Code of 1986, 
as amended (the "Code"), and under applicable state tax law, including, 
without limitation, depreciation deductions under Section 168(b) of the Code, 
and deductions under Section 1631 of the Code in an amount at least equal to 
the amount of interest paid or accrued by Lessor with respect to any 
indebtedness incurred by Lessor in financing its purchase of the Equipment, 
are available to Lessor as a result of the lease of the Equipment.  In the 
event Lessor is unable to obtain such tax benefits as a result of an act or 
omission of Lessee, is required to include in income any amount other than 
the Rent or is required to recognize income in respect of the Rent earlier 
than anticipated pursuant to this Agreement, Lessee shall pay Lessor 
additional rent ("Additional Rent") in a lump sum in an amount needed to 
provide Lessor with the same after-tax yield and after-tax cash flow as would 
have been realized by Lessor had Lessor (i) been able to obtain such tax 
benefits, (ii) not been required to include any amount in income other than 
the Rent and (iii) not been required to recognize income in respect of the 
Rent earlier than anticipated pursuant to this Agreement.  The Additional 
Rent shall be computed by Lessor, which computation shall be binding on 
Lessee.  The Additional Rent shall be due immediately upon written notice by 
Lessor to Lessee of Lessor's inability to obtain tax benefits, the inclusion 
of any amount in income other than the Rent or the recognition of income in 
respect of 

                                      8
<PAGE>

the Rent earlier than anticipated pursuant to this Agreement.  The provisions 
of this Paragraph 33 shall survive the termination of this Agreement.

     34.  GOVERNING LAW; SEVERABILITY.  EACH LEASE SHALL BE GOVERNED BY THE 
LAWS OF THE STATE OF ILLINOIS WITHOUT REGARD TO ITS CONFLICT OF LAW 
PROVISIONS.  IF ANY PROVISION SHALL BE HELD TO BE INVALID OR UNENFORCEABLE, 
THE VALIDITY AND ENFORCEABILITY OF THE REMAINING PROVISIONS SHALL NOT IN ANY 
WAY BE AFFECTED OR IMPAIRED.

     LESSEE ACKNOWLEDGES THAT LESSEE HAS READ THIS AGREEMENT AND THE SCHEDULE 
HERETO, UNDERSTANDS THEM, AND AGREES TO BE BOUND BY THEIR TERMS AND 
CONDITIONS. FURTHER, LESSEE AND LESSOR AGREE THAT THIS AGREEMENT AND THE 
SCHEDULES DELIVERED IN CONNECTION HEREWITH FROM TIME TO TIME ARE THE COMPLETE 
AND EXCLUSIVE STATEMENT OF THE AGREEMENT BETWEEN THE PARTIES, SUPERSEDING ALL 
PROPOSALS OR PRIOR AGREEMENTS, ORAL OR WRITTEN, AND ALL OTHER COMMUNICATIONS 
BETWEEN THE PARTIES RELATING TO THE SUBJECT MATTER HEREOF.

     IN WITNESS WHEREOF, the parties hereto have executed or caused this 
Master Lease Agreement to be duly executed by their duly authorized officers 
as of this 14th day of February, 1997.

                         CUBIST PHARMACEUTICALS, INC.

                         By:  /s/ Thomas A. Shea            
                            -------------------------------
                              Name:     Thomas A. Shea
                              Title:    Director of Finance & Administration



                         Federal Identification Number ###-##-####



                         TRANSAMERICA BUSINESS CREDIT CORPORATION

                         By:  /s/ Gary P. Moro             
                            -------------------------------      
                              Name:     Gary P. Moro
                              Title:    Vice President


<PAGE>

                                                              Exhibit 23.2

                       CONSENT OF INDEPENDENT ACCOUNTANTS

We consent to the incorporation by reference in the registration statements 
of Cubist Pharmaceuticals, Inc., on Form S-3 (File no. 333-33883) and 
Form S-8 (File no. 333-25707) of our report dated January 19, 1998, on our 
audits of the financial statements of Cubist Pharmaceuticals, Inc., as of 
December 31, 1997 and 1996, and for the years ended December 31, 1997, 1996 
and 1995, which report is included in this Annual Report on Form 10-K.

                                       COOPERS & LYBRAND L.L.P.

Boston, Massachusetts
March 18, 1998



<TABLE> <S> <C>

<PAGE>
<ARTICLE> 5
<RESTATED> 
<CIK> 0000912183
<NAME> CUBIST PHARMACEUTICALS, INC.
       
<S>                             <C>                     <C>
<PERIOD-TYPE>                   YEAR                   YEAR
<FISCAL-YEAR-END>                          DEC-31-1997             DEC-31-1996
<PERIOD-START>                             JAN-01-1997             JAN-01-1996
<PERIOD-END>                               DEC-31-1997             DEC-31-1996
<CASH>                                       2,837,600              19,329,353       
<SECURITIES>                                 6,709,623                       0
<RECEIVABLES>                                        0                       0
<ALLOWANCES>                                         0                       0
<INVENTORY>                                          0                       0
<CURRENT-ASSETS>                             9,743,191              20,121,262
<PP&E>                                       5,893,101               4,898,538
<DEPRECIATION>                             (2,712,341)             (1,741,152)
<TOTAL-ASSETS>                              21,673,352              23,452,447
<CURRENT-LIABILITIES>                        1,505,645               2,100,870
<BONDS>                                              0                       0
                                0                       0
                                          0                       0
<COMMON>                                        10,581                   9,544
<OTHER-SE>                                  19,052,085              20,289,066
<TOTAL-LIABILITY-AND-EQUITY>                21,673,352              23,452,447
<SALES>                                              0                       0
<TOTAL-REVENUES>                             2,733,083               4,985,052
<CGS>                                                0                       0
<TOTAL-COSTS>                               12,633,169               8,860,433
<OTHER-EXPENSES>                                     0                       0
<LOSS-PROVISION>                                     0                       0
<INTEREST-EXPENSE>                             237,119                 229,305
<INCOME-PRETAX>                            (7,265,339)             (3,798,669)
<INCOME-TAX>                                         0                       0
<INCOME-CONTINUING>                        (7,265,339)             (3,798,669)
<DISCONTINUED>                                       0                       0
<EXTRAORDINARY>                                      0                       0
<CHANGES>                                            0                       0
<NET-INCOME>                               (7,265,339)             (3,798,669)
<EPS-PRIMARY>                                    (.73)                  (1.49)
<EPS-DILUTED>                                    (.73)                  (1.49)
        

</TABLE>


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